CA2186943A1 - Methods and apparatus for synthesizing labeled combinatorial chemical libraries - Google Patents

Abstract

The present invention provides labeled synthetic libraries of random oligomers and methods and apparatus for generating labeled synthetic oligomer libraries. Each member of such a library is labeled with a unique identifier tag that specifies the structure or sequence of the oligomer. In a preferred embodiment of the present invention the identifier tag is a microchip that is pre-encoded or encodable with information that is related back to a detector when the identifier tag is pulsed with electromagnetic radiation.

Description

wo 96/2406~ 01207 1 ' .

.
Methods and Apparatus for Synt~Pq~7;n~ Labeled Combinatorial Chemistry Libraries The present application is a cnnt;nll~tion-in-part of application Serial No. 08/180,863 filed January 13, 1994, now pending, which is a ~nnt;ml~t;on in part of application Serial No. 08/092,862 filed July 16, 1993, now pending.
FIELD OF THE lNV~N'l'l~N
The present invention relates to labeled combinatorial synthesis libraries and methods and apparatus for labeling individual library members of a cn"~; n~tnrial synthesis library 15 with unique identification tags that facilitate elucidation of the structures of the individual library members synthesized.
BACKGROUND OF THE INVENTION
The relationship between structure and function of 20 molecules is a fundamental issue in the study of biological systems. Structure-function relationships are important in understanding, for exa~ple, the function of enzymes, cellular communication, and cellular control aIId feedback mechanisms.
Certain macromolecules are known to=interact and bind to other 25 molecules having a specific three-f~;r-n~ r~1 spatial and electronic distribution. Any macromolecule having such specificity can be considered a receptor, whether the macromolecule is an enzyme, a protein, a glycoprotein, an antibody, an oligonucleotide sequence of DNA, RNA or the like.
3 0 The various molecules that receptors blnd are known as ligands.
Pharmaceutical drug discovery is one type of research that relies on the study of structure-function relationships. Most contemporary drug discovery involves discovering novel ligands 35 with desirable patterns of specificity for biologically SUBSTITUTE SHEET (F!ULE ~6~

WO96/24061 ~ ~L.'01207 2181i~
~. ~
important receptors. Thus, the time necessary to bring new drugs to market could be: greatly reduced by the discovery of novel methods which allow rapid screening of large numhers of potential ligands.
Since the introduction of solid phase synthesis methods for peptides and polynucleotides new methods employing solid phase strategies have been developed that are capable of generating thousands, and in some cases even millions, of individual peptide or nucleic acid polymers using automated or manual r~r~n;~lP.C, These synthesis strategies, which generate families or libraries of compounds, are generally referred to as "combinatorial chemistry" or "combinatorial synthesis~
strategies . =~
(.~ 1 ;nAtnrial chemistry strategies can be a~~powerful tool for rapidly elucidating novel ligands to receptors of interest.
These methods show particular promise for identifying new therapeutics. See generally, Gorgon et al., "Applications of Combinatorial Technologies to Drug Discovery: II, Com.binatorial Organic Synthesis, Library Screening Strategies, and Future Directions, ~ J. ~d. t'~Pm 37 :1385-401 ~1994~ and Gallop et aI., "Applications of ~Combinatorial Technologies to Drug Discovery: lM Background and Peptide Combinatorial Libraries," J. ~5ed. CB~m 37:1233-51 (1994~. For~xample, combinatorial Iibraries have been used to identify nucleic acid aptamers, Latham et al., "The Application of a Modified Nucleotide in Aptamer Selection- Novel Thrombin Aptamers ~nnt~;n;n~ 5-(1-Pentynyl~-2'-Deoxy Uridine," Nucl. Aci~1q Res.
~:2817-2822 (1994~; to identify RNA ligands to reverse~
transcriptase, Chen & Gold, "Selection of High-Affinity RNA
Ligands~to Reverse Transcriptase: Inhibition of ~cDNA Synthesis and RNase H Activity," Bio~l~Pm;stry ;1;~:8746-56 (1994); and to identify catalytic ~n~;hntl;es specific to a particular reaction transition state, Posner et al., "Catalytic Antibodies:
Perusing Com.binatorial Libraries, " Tr,-nrlc. Bioch~m. Sci.
SUBSTiTUTE SHEET (RULE 26) wo 96/24061 1 ~11~ '01207 218fi~3 145-50 (1994).
The diversity of libraries generated usiny combinatorial strategies is impressive. For example, these methods have been used to generate a library containing four trillion 5 decapeptides, Pinilla ~L., ~Investiyation of Antigen-Antibody Interactions Using a Soluble, Non-Support-Bound Synthetic Decapeptide Library Composed of Four Trillion (4 x 10l~) Sequences, " Biorhrm. J. ~Q~,:847-53 (1994); 1,4-benzodia_epines libraries, Bunin et al., ~The Com.binatorial 10 Synthesis and Chemical and Biological Evaluation of a 1, 4-RGn7r~ 7epine Llbrary, " Proc. ~tl . Acad. Sci. 91:4708-12 (1994) and U.S. Patent No 5,288,514, entitled ~Solid Phase and Combinatorial Synthesis of Benzodiazepine Compounds on a Solid Support," issued Feb. 22, 1994; libraries containing multiple small ligands tiea together in the same molecules, wallace et A Multimeric Synthetic Peptide Combinatorial Library,~
Pent~ R-os. 1:27-31 (1994); libraries of small organics, Chen ~;
al., ''`Analogous' Organic Synthesis of Compound Libraries:
Validation of Combinatorial Chemistry in Small-Molecule Synthesis,~ ,J. Am. Chrm, Soc. ~16:266l-2662 (1994); libraries of peptidosteroidal receptors, soyce & Nestler, ~Peptidosteroidal Receptors for opioid Peptides: Sequence-Selective Binding Using a Synthetic Receptor Library, ~
Chem. Soc. LL~:7955-7956 (1994); and peptide libraries r~nti~;n;n~ non-natural amino acids, Kerr et al., "Encoded Combinatorial Peptide Libraries Containing Non-Natural Amino Acids, " J. Aln. Chem. Soc. 1~ 2529-31 (1993) .
To date, three general strategies for yenerating combinatorial libraries have emerged: "spatially-addressable,~
~split-bead~ and rf~r/ ' ;n~nt strategies. These methods differ in one or more of the following aspects: reaction vessel design, polymer type and composition, control of physical constants such as time, temperature and atmosphere, isolation SUBSTITUTE SI~EET (RULE 2G) WO 96/A061 ~ '^17n7 .

4 ~ ,;
of products, solid-phase or sol-ution-phase methods of assay, simple or complex mixtures, and method for elucidating the structure of the individual library members.
of these general strategies, several sub-strategies have been developed. One spatialIy-addressable strategy that has emerged involves the generation of peptide libraries on immobilized pins that fit the dimensions of standard microtitre plates. S~ PCT Publication Nos. 91/17271 and glrl98l8, each of which is incorporated herein by referçnce. This methQd has been used to identify pçptides which mimIc discon~inuous epitopes, Geysen et al., BioM.~. Ohf~m. Lett. 3 :391-404 ~1993), and to generate benzodiazepine libraries, U. S . Patent No.
5,288,514, entitled ~Solid Phase=and Combinatorial Synthesis of senzo~ 7~ P r~ rlq on a Solid Support, ~ issued ~eb. 22, 1994 and sunin ~, ~The Combinatorial Synthesis and Chçmical and siological Evaluation of a 1, 4-senzodiazepine Library,~ Proc. Natl. Acad. Sci. .~1:4708-12 (1994). The structures of the individual library members can be decoded by analyzing the pin location-in con~unction with the segue.nce of reaction s~eps used :during the synthesis.
A second, related spatially-addressable strategy that has emerged involves solid-phase synthesis of polymers in individual' ~ reaction vessels, where the ihdividual vessels are arranged into a single reaction~ unit. An ilIustrative example of such a reaction unit is a standard 96-well microtitre plate;
the entire. plate comprises the reaction unit and each well corresponds to a single reaction vessel. This approach is an extrapolation of traditional single-column solid-phase synthes is .
As is exemplified by the 96-well: plate reaction unit, each reaction vessel is spatially defined by a two-dimensional matrix. ~hus, the structures of individual library members can be decoded by analyzing the seguence of reactions to which each well was subj ected.
SUBSTITUTE SHEET (RULE 26) WO 96/2406 I PCTlbS96/01207 ;e.tl~6s~
Another spatially-addressable strategy employs ~ tea bags to hold the synthesis resin. The reaction sequence to which each tea bag is subject is recorded, which determines the structure of the oligomer synthesized in each tea bag. See for example, Lam ~;L, "A New Type of Synthetic Peptide Library for Identifying Ligand-Binding Activity, u I~ ~: 82-84 (1991); Houghten ~,, "Generation and Use of Synthetic Peptide Combinatorial Libraries for Basic Research and Drug Discovery, " ~a~ 354: 84-86 (1991); Houghten, "General Method for the Rapid Solid-Phase Synthesis of Large Numbers of Peptides: Specificity of Antigen-Antibody Interaction at the Level of Individual Amino Acids," Proc. Natl. Acad. Sci.
~2:5131-5135 (1985); and Jung et al., Aanew. Chem. Int. Ed.
Enrl. q1 :367-383 (1992), each of which is incorporated herein by reference.
In another recent development, scientists rt h; nr~ the techniques of photolithography, chemistry and biology to create large collections of oligomers and other compounds on the surface of a substrate (thls method is called "VLSIPS~
~, for example, U.S. Patent No. 5,143,854; PCT Publication No. 90/15070; PCT Publication No. 92/10092 entitled "Very Large Scale Trmnnh;l;~ed Polymer Synthesis," June 25, 1992; Fodor et al., "Light-Directed Spatially Addressable Parallel Chemical Synthesis," Science ~1:767-773 (1991); Pease et al., "Light-Directed Oligonucleotide Arrays for Rapid DNA Sequence Analysis, " Proc. Natl. Acad. Sci. 91:5022-5026 (1994); and Jacobs & Fodor, "Combinatorial Chemistry: Applications of Light-Directed Chemical Synthesis, " Trt~nt~q. Bioterhnnloav lZ(l) :19-26 (1994), each of which is incorporated herein by 3 0 ref erence .
Others have developed rer~ ~ ;n~nt methods for preparing collections of oligomers. See, for example, PCT Publication No. 91/17271; PCT Publication No. 91/19818; Scott, "Discovering SUBSTITUTE SHEEr (RULE 26,~

WO 96/24061 ~ , C.'0l207 Peptide Ligands Using Epitope Li~a~r~e~s~ ~ 17: 241-245 (1992); Cwirla ~, ~Peptides on Phàgè: A Vast Library of Peptides for Identifying Llgands, ~ Proc. Natl. Acad. Sci.
87: 6378-6382 (1990) i Devlin ~L~ Random Peptide Libraries:
5 A Source of Specific Protein 13inding Molecules," ~i~n5~
249:404-406 (1990); and Scott & Smith, "Searching for Peptide Ligands with an Epitope Library," Science .2~:386-390 (1990).
Using these methods, one can identify each oligomer in the library by detPrm;nin~ the coding sequences in the recombinant 10 organism or phage. I~owever, since the library members are generated in vivo, recl h;n~nt methods are limited to polymers whose synthesis is mediated in the cell. Thus, these methods typically have been restricted to constructing peptide libraries .
A third general strategy that has emerged involves the use of ~split-bead~ combinatorial synthesis strategies. ~, for example, Furka et al., Int. ~. Pe~t. Prote;n R~. 37:487-493 (1991), which is incorporated herein by reference. In this method synthesis~supports are apportioned into aliguots, each 20 aliquot exposed to a monomer, and the beads pooled. The beads are then mixed, reapporeioned:into aliquots, and exposed to a second monomer. The process is repeated until the desired library is generated.
Since the polymer libraries generated with the spllt-bead 25 method are not spatially-addressable, the structures of the individual library members~cannot be elucidated hy analyzing the reaction histogram. Rather, structures must be determined by analyzing the polymers directly. Thus, one limitation of the split-bead approach is the requisite for an available means 30 to analyze the polymer composition. While sequencing techniques are availahle for peptides and nucleic acids, sequencing reactions for polymers of other composition, such as for example carbohydrates, organics, peptide nucleic acids or mixed polymers may not be readily known.
SUBSTITUTE SHEET (RULE 26~

WO 96/24061 ~ 1 ~ 6 g q 3 1 ~ ., ~,~, L.'0 1207 ....

Variations on the ~split-bead~ scheme have emerged that obviate the need to sequence the library mem.ber directly.
These methods utilize chemicals to tag the growing polymers with a unique identification tag ( ~co-synthesis~ strategies) .
~, for example, PCT Publication No. WO 94/08051 entitled ~Complex Combinatorial Chemical Libraries Encoded with Tags,"
April 14, 1994; Nestler ~L., "A Ge]~eral Method for Molecular Tagging of Encoded Combinatorial Chemistry Libraries, ~ J. Orc.
Chem. 59:4723-4724 (1994); PCT Publication No. Wo 93/06121 entitled ~Method of Synth~q;7ing Diverse Collections of oligomers, ~ April 1, 1993; Needels ~ aL.. Proc. ~Atl ArA~l .
~S.il. 90:10700-10704 (1993); Kerr çt al., "Encoded Combinatorial Peptide Libraries C~n~A;n;n~ Non-Natural Amino Acids,~ J, Am~r m Soc. 11~:2529-2531 (1993); and 13renner & Lerner, ~Encoded Combinatorial Chemistry,~ Proc. ~Atl. Acad. Sci. 89:5381-5383 (1992), each of which is incorporated herein by reference.
~n~ntl;n~ library members with chemical tags occurs in such a fashion that uni~aue identifiers of the chemical struc~ures of the individual library members are co11structed in parallel, or are co-synthesized, with the library members. Typically, in a linear three component synthesis containing ouilding blocks A, B and C in the process of generating library member AsC, an encoding tag is introduced at each stage such that the tags T, TE and TC would encode for individual inputs in the library.
The synthesis would proceed as follows: (a) ~'~f'm;~-A~ A is coupled onto a synthesis bead, immediately followed by coupling tag T~ to the bead; (b) The bead is subject to deprotection conditions which remove the protecting group selectively from A, leaving TA protected. Chemical B is coupled to the bead, 30 generating the sequence As~ The bead is then subject to deprotection which selectively removes the protecting group from TA~ and T,3 is coupled to the bead, generating tag sequence T TE; (c) The third component C and concomitant tag T is added to the bead in the manner described above, generating library Wo 96124~6~ ,6~ n7

2~8fi9~3 i`
sequence AsC and tag se~uence T~T~3TC- ~5 For large libraries rnnt~;ni,r~three chemical= inputs, the chemical tagging ser~uence is the same. Thus, to generate a large library cnnt~in;nr the complete set~of three-input, one hundred unit length polymers, or 1003=106 library members, uni~ue identifying tags are introduced such that there is a uniQue identifier tag for each different chemical structure.
Theoretically, this method is applicable to libraries of any complexity as long as tagging sequences can be developed that have at least the same number of identification tags as there~
are numbers of unir~ue chemical structures in the library.
While combinatorial synthesis strategies provide a powerful means for rapidly identifying target molecules, substantial problems remain. For example, since members of spatially addressable libraries must be synthesized in spatially segregated arrays, onIy relatively small libraries can be constructed. The pPsition o~ each reaction vessel in a spatially-adaressable library is defined by an XY coordinate pair such that the entire llbrary is~ defined by a two-dimensional matrix. AS the size of the library increases the dimensions of the two-dimensional matrix increases. In~
addition, as the number of different transformation events used to co~struct the library increases linearly, the library size increases exponentially. Thus, while generating the complete set of linear tetramers comprised of four different inputs rer~uires only a 16x16 matrix (44=256 library members~, generating the cPmplete set of linear octamers composed of four diffe~ent inputs requires a 256x256 matrix (4P=65~,536 liQrary members), and generating the complete set of linear tetramers composed of twenty different inputs rer~uires a 400x400 matrix ~204=160,000 library membersr. Therefore, not only does the physical size of the library matrix r~uickly become. unwieldy (constructing the c.Dmplete set Qf linear tetramers composed of twenty different inputs using sgatially-addressable techniques requires 1667 microtitre plates)~, delivering reagents to each SUBSTITUTE SHEET (RULE 26) wo 96/2406~ 01207 2186~4~
.

reaction vessel in the matrix re~uires either tedious, time-consuming manual manipulations, or complex, expensive automated equipment .
While the :VLSIPSlM method attempts to overcome this 5 limitation through miniaturization, V~SIPSTM requires specialized photoblocking chemistry, expensive, specialized synthesis equipment and expensive, specialized assay etIuipment.
Thus, the VLSIPSTtd method is not readily and economically adaptable to emerging solid phase chemistries and assay 10 methodologies.
Split bead methods also suffer severe limitations.
Although large libraries can theoretically be constructed using split-bead methods, the identity of ] ibrary members displaying a desirable property must be detPrm; n~ by analytical 15 chemistry. Accordingly, split-bead methods can only be employed to synthesize compounds that can be readily elucidated by microscal e sequencing, such as polypeptides and polynucleotides .
Co-synthesis strategies have attempted to solve this 20 structure elucidation problem. However, these methods also suffer limitations. For example, the tagging structures may be incompatible with synthetic organic= chemistry reagents and conditions. Additional limitations follow from the necessity for compatible protecting groups which allow the alternating 25 co-synthesis of tag and library member, and assay confusion that may arise from the tags selectively binding to the assay receptor.
Finally, since methods such as the preceding typically require the addition of like moieties, there is substantial 30 interest in discovering methods for producing labeled libraries of compounds which are not limited to sequential addition of like moieties, and which are amenable to any chemistries now known or that will be later developed to generate chemical libraries. Such methods would find application, for example, 35 in the modification of steroids, sugars, co-enzymes, enzyme SUBSTITUTE SHEET (RllLE 2~

W096~2406~ 6943 . PCT/US96101207 inhibitors, ligands and the like, which fre~uently involve a multi-stage synthesis in which one would wish to vary the reagents and/or conditions to provide a variety of compounds.
In such methoas the reagents may be organic ~or inorganic 5 reagents, where functionalities or side groups may be =~
introduced, removed or modified, rings opened or closed, stereochemistry changed, and the like.
From the above, one can rec~ognize that there is substantial interest in developing improved methods and l0 apparatus for the synthesis of complex labeled combinatorial chemical libraries which readily permit the construction of libraries of virtually any composition and which readily permit accurate structural determination of individual compounds within the library that are identified as being of interest.
15 Many of the disadvantages of the previously-described methods as well as many of the needs not met hy them are addressed by the present inueIltion, which as described more fully hereinafter, provides myriad advantages ove-r these previously-described methods.
GLOSSARY
The folIowing terms are; nt~n~f~tl to have the following general meanings as~ they are used herein: ~
L~heled Svnt~t;c Oliqorn~r ~hr~lrv: A ~labeled synthetic oligomer~ library~' is a collection of random synthetic oligomers wherein each member of such a library is labeled with a unique identifier tag from which the structure or sequence of each oligomer can be deduced~
I~nti fi~r Ta~: An ~identifier tag" is any detectable attribute that provides a means whereby one can elucidate the structure of an individual oligomer in a labeled synthetic oligomer library. Thus, an identifier tag identifiçs which tra~sformation events an individual oligomer has experienced in SUBSTITUTE SHEET (RULE 26) Wo 96l24061 . ~~ 0l207 ~18694~
the synthesis of a labeled synthetic oligomer library, and at which reaction cycle in a series of synthesis cycles each transf ormation event was experienced.
An identifier tag may be any detectabIe feature, ; nr~ ; n~, for example. a dif ferential absorbance or emission of light; magnetic or electronically pre-encoaed information;
or any other distinctive mark with the required information.
An lfl~nt;fier tag may be pre-encoded with unique identifier information prior to synthesis of a labeled synthetic oligomer library, or may be encoded with a identifier information in concomitant with synthesis of a labeled synthetic oligomer library.
In this latter embodiment, the iaentifier information added at each synthesis cycle is pre~f erably added in a lS sequential fashion, such as, for example digital information, with the identifier information identifying the transformation event of synthesis cycle two being appended onto the identifier information identifying the transformation event of synthesis cycle one, and so forth.
Preferably, an identifier tag is impervious to the reaction conditions used to construct the labeled synthetic oligomer library .
A preferred example of an identifier tag is a microchip that is pre-encoded or encodable with information, which information is related back to a detector when the microchip is pulsed with electromagnetic radiation.
Pre-En~oded I~ntifier Taq: A ~pre-encoded identifier tag~ is an identifier tag that is pre-encoded with uni~ue identifier information prior to synthesis of a labeled synthetic oligomer library. A preferred example of such a pre-encoded identifier tag is a microchip that is pre-encoded with information, which information is related back to a detector when the microchip is pulsed with electromagnetic radiation.
SU~STITUTE SHEET (RULE 26) Wo 96n4061 Pcrluss6lol2o7 2186g43 ';
~2 ~nrodAhle Id~ntifi~r Tac: An ~encodable identifier tag~
is an identifier tag that is capable of recelving identifier information from time to time. An encodable identifier tag may 5 or may not be pre-encoded with partial or complete identifier information prior to synthesis of a labeled synthetic oligomer library. A preferrea example of such an encodable identifier tag is a microchip that is capable of receiving and storing information from time to time, which i~formation is related 10 back to a detector when the microchip is pulsed with ele~:L~ ~ rn~tiC radlation.
Tr~n~fo~r~tion Event: As used herein, a ~transformation event~ is any event that results in a change of chemical 15 structure of an oligomer or polymer. A ~transformation event~
may be mediated by physical, chemical, enzymatic, biological or other means, or a r~ ' ;n;lt;nn o~ means, 1nr~u~1;n~ but not limited to, photo, chemical, enzymatic or biologically mediated isomerization or cleavage; photo, chemical, enzymatic or 20 biologically mediated side group, or functional group addition, removal or modification; changes~ in temperaturei~changes in pressure; and the like. Thus, ~~transformation event~ includes, but is not limited to, events that result in an increase in molecular weight of an oligomer or polymer, such as, for 25 example, addition of one or a plurality of monomers, addition of solvent or gas, or coordlnation of metal or other inarganic substrates such as, for example, zeolities; events that result in a decrease i~ molecular weight of an oligomer=or polymer, such as, for: example, de-hydrogenation of- an alcahol to from an 30 alkene or enzymatic hydrolysis af an ester or amlde; events that result in no ~et change in molecular weight of an oligomer or polymer, such as, for example, stereochemistry changes at one or a ~lurality of a chiral centers, Claissen rearran-gement, or ~ope rearrangement; and other events as will become apparent 35 to those skilled in the art upon review of this disclosure.
SIJBSTITUT~ SHEET ~R' I LE 2~) `

WO 96/24061 i ~ Lv~ L!Dl2D7 21869q3 13 ~, for example, application Serial No. 08/180, 863 filed January 13, 1994, which is assigned to the assignee of the present invention and PCT Publication WO 94/08051 entitled "Complex Combinatorial Libraries Encoded with Tags,~ April 14 5 (1994), each of which is incorporated herein by reference.
~ 5Q~m~: As used herein, a " ~' is any atom or molecule capable of forming at least one chemical bond. Thus, a ~monomer~ is any member of the set of atoms or molecules that 10 can be joined together as single units in a multiple of se~uential or concerted chemical or enzymatic reaction steps to form an oligomer or polymer. Mnn~ s may have one or a plurality of functional groups, which functional groups may be, but need not be, identical.
The set o~ - :, useful in the present invention includes, but is not restricted to, alkyl and aryl amines;
alkyl and aryl mercaptans; alkyl and aryl ketones; alkyl and aryl carboxylic acids; alkyl and aryl esters; alkyl and aryl ethers; alkyl and aryl sulfoxides; alkyl and aryl sulfones;
20 alkyl and aryl sulfonamides; phenols; alkyl alcohols; alkyl and aryl alkenes; alkyl and aryl lactams; alkyl and aryl lactones;
alkyl and aryl di- and polyenes; alkyl and aryl alkynes; alkyl and aryl unsaturated ketones; aldehydes; sulfoxides; sulfones;
heteroatomic compounds cnnt~-n~n~ one or more of the atoms of:
25 nitrogen, sulfur, phosphorous, oxygen, and other polyfunctional molecules cnntilining one or more of the above functional groups; L-amino acids; D-amino acids;
deoxyribonucleosides; deoxyribonucleotides; ribonucleosides;
ribonucleotides; sugars; benzodiazepines; ~- lactams;

3 0 hydantoins; suLnones; hydroS~uinones; terpenes; and the like .
The monomers of the present invention may have groups protecting the functional groups within the monomer. ~uitable protecting groups will depend on the functionality and particular chemistry used to construct the library. Examples SUE~STITUTE SHEET (RULE 26) WO 96~4061 PCr/US96/01207 ~1869 43 ;
1~ ~
of suitable functional protec~ grou,os will be readily apparent to skilled artisans, and are descri~ed, for exampIe, in Greene and Wutz, Protectin~ rrOu~s in Ora~n~c Svn~hPqi~, 2d ed., John Wiley ~ Sons, ~Y (l99l), which is incorporated herein 5 by ref erence, As used herein, ~monomer~ refers to any member of a basis set for synthesis 4f an oligomer. For example, dimers of 1.-=
amino acids form a basis set oi~ ~00 ~ for synthesis of polypeptides. Di~ferent basls sets of monomers may be used at lO successive steps in the synthesis of a polymer. ~ ~
oli( -r or PolvmPr: As used herein, an ~oligomer~ or ~polymer~ is any chemical structure that can be synthesized using the combinatorial library methods of this invention, 15 including, for example, amides, esters, thioethers, ketones, ethers, sulfoxides, sulfnn~miriP~, sulfones, phosphates, alcohols, aldehydes, alkenes, alkynes, aromatics, polyaromatics, heterocyclic compounds containing one or=~ more of -the atoms of: nitrogen, ~ sulfur, oxygenC and phosphorous, and 20 the like; chemical entities having a çommon core-~structure such as, for example, terpenes, steroids, ,~-ractams, bPn7o~i~7epines, xanthates, indoles, indolones, Iactones, lactams, hydantoins, auinones, hydro~auinones, and the like;
chains of repeating monomer units such as polysaccharides, 25 phospholipids, polyurethanes, polyesters, polycarbonates, poly ureas, polyamides, polyethyleneimines, poly arylene suIfides, polyimides, polyacetates, polypeptides, polynucIeotides, and the like; or other oligomers or~ polymers as~ wilI be readily apparent to one skilled in the art upon review of this`
30 disclosure. Thus, an ~oligomer~ and ~polymer~' of the ~oresent invention may be linear, branched, cyclic, or assume various other forms as will be apparent to those skilled in the art.
rnnnprted: As used herein ~'concerted" means synchronous SUBSTITUTE SHEET (RULE 26) WO 96/24061 2 1 8 6 ~ 4 3 PCrlUSg6101207 , ~

and asychronous formation of one or more chemical bonds in a single reaction step.
Suhstrate: As used herein, a ~substrate~ is a synthesis 5 means linked to an identifier tag. By way o~ example and not limitation, a ~substrate~ may be an identifier tag functionalized with one or a plurality of groups or linkers suitable for synthesis; a glass or polymer encased identifier tag, which glass or polymer is functionalized with one or a 10 plurality of groups or linkers suitable for synthesis; an identifier tag-that is coated with one or a plurality of synthesis supports; an identifier tag retained within a frame or housing, which frame or housing is functionalized with one or a plurality of groups or linkers suitable for synthesis; an 15 identifier tag retained within a frame or housing, which frame or housing also retains one or a plurality of synthesis supports; and the like.
Synt~esis pl~An.~: A ~synthesis means~ is any means for 20 carrying out synthesis of a Iabeled synthetic oligomer library.
Thus, ~ synthesis means ~ may comprise reaction vessels, columns, capillaries, frames, housings, and the like, suitable for carrying out synthesis reactions, one or a plurality of synthesis supports suitable for carrying out synthesis 25 reactions; or functional groups or linkers attached to an identifier tag suitable for carrying out synthesis reactions.
"Synthesis means~ may be constructed such they are capable of retaining identifier tags and/or synthesis supports.
In a preferred: h of~;mpnt a ~synthesis means~ is one or a 30 plurality of synthesis supports.
Svnthesis Su~ort: A "synthesis support" is a material having a rigid or semi-rigid surface and having functional groups or linkers, or that is capable of being derivatized with SUBSTITUTE SHEET ~RULE 26?

3 ~ 7 16 ~ ?:
functional groups or linkers, that âre suitable for~ car~ing out synthesis reactions.
Such materials will preferably take the form of small beads, pellets, disks, capillaries, hollow fIbers, needles, solid fibers, cellulose beads, pore-glass beads, silica gels, polystyrene beads optlo~ally cross-linkea with polyethylene glycol divinylbenzene, :yrafted co-poly beads, poly-acrylamide~ .
beads, latex beads, dimethylacrylamide beads optionally cross-linked with N,N~-bis-acryloyl ethylene diamine, glass particles coated with a hydrophobic polymer, or othe'r~'convenient forms.
~Synthesis supports~ may be constructed such that they are capable of :retaining ide~tifier tags.
IL~k~: A ~linker~ is a molety, molecule, or group of molecules attached to a synthësis support or substrate and spacing a synthesized polymer or oligomer from the synthesis support or.substrate. A ~linker'~ can also be a moiety, molecule, or yroup of molecuIes attached to a substrate =and spacing a synthesis support from the substrate.
Typically a linker wïll be bi-functionaI, whërein said linker has a functional group at one end capable of attaching to a monomer, oligomer, synthesis support or substrate, a series of spacer residues, and a functionaL group at another end capable of attaching to a monomer, oligomer, synthesis support or substrate. The functional groups may be, but need not be, identical.
SDacPr r~eiduPq: ~Spacer residues~ are atoms or molecules positioned between~ the functio~al groups of a bifunctional linker, or:-~between a functional group of a linker~ and the moiety to which the linker is attached. ~iSpacer residues~ may be atoms capable of forming at least two covalent bonds such as carbon, silicon, oxygen, sulfur, phosphorous, and the like, or may be molecules capable of forming at least two covalent bonds 3 5 such as amino acids, peptides, nucleosides, nucleotides, SUBSTITUTE SHEET (RULE 2fi!

WO96124061 ~ ~ n7 21 869~3 ` " -sugars, carbohydrates, aromatic rings, hydrocarbon rings, linear and branchea hydrocarbons, and the like.
Linked together the spacer residues may be rigid, semi-rigid or flexible. Linked spacer residues may be, but need not 5 be, identical.
Pre-,=nrnded Sllh~trate: A "pre-encoded substrate~ is a substrate wherein the ;~lPnt;f;er tag is a pre-encoded identifier tag.
~ n~ n~1~hle Sllhstrate: An ~encodable substrate" is a substrate wherein the ;~f~nt;~;er tag is an encodable identifier tag .
Synth~tic: A compound is ~ synthetic ~ when produced by in itro chemical or enzymatic synthesis.
oli~ ^r or Polv~n~r Se~u~n~e: As used herein ~oligomer sequence~ or '~polymer sequence~ refers to the chemical 20 structure of an oligomer or polymer.
SUMM~RY ~ OF T~E lNVl~;N'l'l~N
The present invention relates to labeled libraries of random oligomers. Each library member is Iabeled with a unique 25 identifier tag from which the structure of the library member can be readily ascertained.
The present invention also relates to methods and apparatus for synth~Q;7;n~ labeled libraries of random oligomers. The random oligomers are generally synthesized on 30 synthesis supports, but may be cleaved from these supports or synthesized in solution phase to provide a soluble library. In a pref erred embodiment the oligomers are composed of a set of monomers, the monomers being any member of the set of atoms or molecules that can be~: joined together to form an oligomer or SUBSTITUTE SHEET (RULE 26~

WO 96/24061 t ., r~ C1207 218fi943 18 polymer. : The library is then screened to isolate individual nl; 5 b that bind to a receptor or possess some desired property. In a preferred embodiment, each oligomer structure in the library is unir~ue.
The identifier tag is used to identify the structures of oligomers rrnt;l;nl~d in the labeled synthetic oligomer library.
The identifier tag, which may be linked to the oligomer in a variety of fashions, may be any detectable feature that in some way carries the rer"uired information, a~d that is decipherable.
Preferably, the identifier tag is impervious to the chemical reagents used to synthesize the~library.
In a preferred embodiment the identifier tag relates a signal to a detector upon excitation with electromagnetic radiation. Suitable identifier~tags may be, by way of example and not limitation, bar codes that can be scanned with a laser, chemical moieties that differentially emit or absorb light, such as chromophores, fluorescent, and phosphorescent moieties, or microchips that are pre-encoded or are encodable with a unio~ue radiofreo,uency ~ fingerprint~ that emit a detectakle 2(~ signal when pulsed with elec~cromarJnetic radiation.
In a further preferred embodiment the identification tags are encased in glass or a polymeric material that can be coated with synthesis supports or derivatized with functional groups or li~kers suitable for synthesls. Preferably, the identifier tags can be sorted with automatic sorting er,~ ^nt Such polymeric ~ materials and sorting er~uipment are widely known in the art.

SUBSTITUTE SHEET (RULE 26) " ' ~ \ ! I '' ~ ' WO 96/2d61 218 6 g 4 3 P ~ 'U12D7 BRIEF DESCRIPTION OF THE FIGURES
Figure l schematically illustrates the synthesis of the complete set of linear trimers composed of four different monomer inputs using pre-encoded identifier tags.
Figure 2 schematically illustrates the assembly of the complete set of linear trimers composed of four different monomer inputs wherein the identifier tags are encoded with identifier information in parallel with oligomer synthesis.
Figure 3 schematically illustrates the synthesis of a labeled library of oligomers composed of four different monomer inputs and having a common core structure using pre-encoded i dent i f i er tags .
Figure 4 5rh~ t;r;~lly illustrates the synthesis of a labeled library of oligomers composed of four different monomer l~ inputs and having a common core structure wherein the identifier tags are encoded with identifier information in parallel with oligomer synthesis.
Figure 5 schematically illustrates the synthesis of a labeled library of oligomers constructed u5ing a multiple cycle synthesis series with a plurality of different transformation events using pre-encoded identifier tags.
Figure 6 schematically illustrates the synthesis of a labeled library oligomers constructea using a multiple cycle synthesis series with a plurality of different transformation events wherein the identifier tags are encoded in parallel with oligomer synthesis.
Figure 7 schematically illustrates several ways in which an identifier tag can be linked to an oligomer library member.
n~TATT ~n DESCRIPTIOM OF THE INVENTION
The present invention provides labeled synthetic libraries of random oligomers and methods and apparatus for generating labeled synthetic oligomer libraries. Each member of such a library is labeled with a unique identifier tag that specifies the structure or sequence of the oligomer. In a preferred SUBSTITllTE SHEET (RULE 26) Wo 96/24061 PcrNS96101207 2186943 Il:
20 ~ ,'~ ', emoodiment of the present invention the identifier tag Is a microchip that is pre-encoded or encodàble with information that is related back to a detecEor when the identifier tag is pulsed with electromagnetic radlation.

. T.Ahel ed Ol; ~ T.~hr~rie~
The present invention relates to labeled libraries of ::
random oligomers. Each member of a random oligomer library is linked to:~an identifier~ tag such that the structure of the lO oligomer library member can be readily ascertained. The random oligomer library generally comprises a highly diverse collection of oligomers, wherein each member of such library comprises a single oligomer structuFe (e.g., a bl~:n7r)~1~A7epine).
The oligomers may be soluble or may be bound to a synthesis 15 support or substrate.
The library members may be linkea to an identifier tag in a variety of fashions. ~ç, for example~ Figure 7. For example, an oligomer library member may be attached to a synthesis support, which synthesis support is retained within a 20 reaction vessel, frame or housing that also retains an identifieF tag. As another example, a library member~m~ay be attached to a synthesis support which is in turn attached to an identifier tag . The library member may be attached directly ~ to a functional group on the synthesis support~ but will usually 25 be attached by means of a linker. The linker will generally be a bi-functional linker, which bi-functional linker comprises a functional group capable of attaching to a monomer, oligomer, synthesis support or substrate on one end, a series of ~spacer residues, and a functional group capable of attaching to a 30 monomer, oligomer or synthesis support or substrate at another end .
Attachment of a synthesis support to an identifier tag can be mediated by a variety of means. For` example, an idehtifier tag may be coated with one or a- plurality of synthesis:
35 supports, which synthesis supports are attached ~to the SUBSTITUTE SHEET (RULE 26) Wo 96/24061 P~""~ 7 i9~3 21 identifier tag by physical means such as glue or magnetic attraction. In one embodiment a synthesis support may be a polymer capable of being functionalized with reactive groups or linkers, which synthesis support is molded into a frame or 5 housing that retains an identifier tag.
Alternatively, one or a plurality of synthesis supports may be covalently attached to an identifier tag. Covalent attachment may be directly to a functional group on the identifier tag, or may be mediated by a linker as described l 0 above .
In another embodiment, a library member may be attached directly to a functional group on an identifier tag, or to a linker which is attached to a functional group on an identifier tag .
Synthesis supports and substrates may have a plurality of functional groups or linkers, such that each synthesis support or substrate may have a plurality of oligomer library members of identical sequence attached thereto. The ~uantity synthesized of each library member comprising the labeled 20 oligomer library can be varied by varying the number of synthesis supports, functional groups or linkers on synthesis supports, or functional groups or linkers on substrates. ThuS, the labeled oligomer library of the present invention may comprise milligram quantities of each library member structure, 25 thereby providing a sufficient quantity of each library member for multiple assays or other analytical experiments.
The labeled oligomer libraries of the present invention generally comprise a highly diverse collection of oligomers.
Such a library may contain, for example, all N different 3 0 oligomers, wherein each oligomer is synthesized in a series of X synthesis cycles using N different transformation events. As a specific example, a library may contain all combinations of x different oligomers, which oligomers are composed of N
different I b assembled in x synthesis cycles.
SUeSTlTUTE SHEET (RULE 26~

W0 96r2406~ 7n7 ~ 2;2~
The library may aIso contài~oligomers having been synthesized with different transformation events at, for example, only one or a small number of cycles irl the synthesis series, while having identical transformation events at all 5 other cycles. As a specific example, a library may contain oligomers having different monomers at only one or a small number of positions while having identical monomers at all other positions.
oligomers Dr polymers of the present invention are formed 10 from a stepwise or concerted series of tra~sformation events.
A transformation event is any event that results in a change of chemical structure of an oligDmer or polymer. A transformation event may be mediated by physical, chemical, enzymatic, biological or other means, or a combination of means, including 15 but not limited to, photo, chemical, enzymatic or biologically mediated isomerization or cleavage; photo, chemical, e~ymatic or biologically mediated side group or functional group addition, removal or modification; changes in temperature;
changes in pressure; and the like. Thus, transformation events 20 include,~but are not lImited to, events that resuit iII~an increase in molecular weight of an oligomer or polymer, such as, for example, addition of one or a plurality of mor~omers, addition of solvent or gas, or ~coordination of metal or other inorganic substrates such as, for example zeolities; events 25 that result in a decrease in molecular weight of an oligomer or polymer, such as, for example, dehydrogenation of an alcohol to from an alkene, or enzymatic hydrolysis of an ester or=amide;
events that result in no net change in molecular weight of an oligomer or polymer, such as, for example, stereochemistry 30 changes at one or a plurality o:f a chiral centers, Claissen rearrangement, or Cope rearran~ement; and other events as will become apparent to tkose skilled in the art uporl review of this disclosure. ~:, for example, application Serial No. ~
08/180, 8~ ~iled January 13, 1994, which is assigned to the 35 assignee of= the present invention and PCT Publication W0 SU~STITUTE SHEET (RULE 26) Wo 96/24061 2 1 8 6 9 4 3 ' - Y~" ~ ~A7 94/08051 entitled "Complex Combinatorial Libraries Encoded wit~
Tags,~ April 14 (1994), each of which is incorporated herein by ref erence .
In a preierred embodiment, at lease one transformation 5 event in the generation of a labeled synthetic oligomer library is the stepwise or concerted enzymatic or chemical addition of one or a plurality of ~ ~
In another preferred embodiment, each transformation event in the generation of a labeled synthetic oligomer library is 10 the stepwise or concerted enzymatic or chemical addition of one or a plurality of monomers.
A monomer is any atom or molecule capable of forming at least one rhPm;r;31 bond. Thus, a monomer is any member of the set of atoms or molecules that can be joined together as single 15 units in a multiple of seguential or concerted chemical or enzymatic reaction steps to forma an oligomer or polymer. The set of monomers useful in the present invention ~nrl~ , but is not restricted to, alkyl and aryl amines; alkyl and aryl mercaptans; alkyl and aryl ketones; alkyl and aryl carboxylic 2 0 acids; alkyl and aryl es ters; alkyl and aryl ethers; alkyl and aryl sulfoxides; alkyl and aryl sulfones; alkyl and aryl sulfonamides; phenols; alkyl alcohols; alkyl and aryl alkenes;
alkyl and aryl lactams; alkyl and aryl lactones; alkyl and aryl di- and polyenes; alkyl and aryl alkynes; alkyl and aryl 25 unsaturated ketones; aldehydes; sulfoxides; sulfones;
heteroatomic compounds containing one or more of the atoms of:
nitrogen, sulfur, phosphorous, oxygen, and other polyfunctional molecules ~nnt~n;ng one or more of the above functional groups; L-amino acids; D-amino acids;
3 0 deoxyribonucleosides; deoxyribonucleotides; ribonucleosides ribonucleotides; sugars; benzodiazepines; ¦3-lactams;
hydantoins; quinones; hydro(Iuinones; terpenes; and the like.
The mnn ~i of the present invention may have groups protect3~g the functional groups within the monomer. Suitable SUBSTITUTE SHEET (RULE 26) Wo 96/24061 , i: PCr/US96/01207 218fi9~3 protecting groups will depend on the functionality and particular chemistry used to construct the library. Examples of suitable functional protecting grouE~s will be readily apparent to skilled artisans, and are described, for example, 5 in Greene and Wutz, Protectin~ ('.rou~s in Or~TAn; c SyntllP~is, 2d ed., John Wiley & Sons, NY (1991), which is incorporated herein by reference.
As used herein, monomer refers to any member of a basis set for synthesis of an oligomer. For example, dimers of L~
10 amino acids form a basis set of 400 "~ for synthesis of polypeptides. Different basis sets of monomers may be used at successive steps in the synthesis of a polymer. Thus, as the skilled artisan will appreciate, the oligomer or polymer library members generated by practicing the present invention 15 may serve as -- ~ a in a the synthesis of a la~eled synthetic oligomer libraries.
Accordingly, oligomers or polymers of the present invention comprise any chemical structure that can be synthesized using the combinatorial library methods of this 20 invention, including, for example, amides, esters, thioethers, ketones, ethers, sulfoxides, sulfonamides, sulfones, phosphates, alcohQls, aldehydes, a~lkenes, alkynes, arom=atics, polyaromatics, heter~cyclic compounds containing one or= more of the atoms of: nitrogen, sulfur, oxygen, and phosphorous, and 25 the like; chemical entities having a common core structure such as, for example, terpenes, steroids, ,3-lactams, benzo~;A7Pr;npc~ xanthates, indoles, indolones, lactones, lactams, hydantoins, quinones, hydroquinones, and the like;
chains of repeating monomer units such as polysaccharides, 3 0 phospholipids, polyurethanes, polyesters, polycarbonates, poly ureas, polyamides, polyethylPnplm;npc~ poly arylene sulfides, polyimides, polyacetates, polypeptides, polynucleotides, and the like; or other~oli~omers or polymers as will- be readily apparent to one skilled in the art upon review of this SUEISTITUTE SHEET (RULE 26!

WO96/24061 ?1~6!143 ~ 01207 disclosure. Thus, an ~oligomer'~ and "polymer~ of the present invention may be linear, branched, cyclic, or assume various other forms as will be apparent to those skilled in the art.
A labeled oligomer library of t~le present invention may 5 comprise virtually any level o f complexity and is limited in size only by the physical size of a substrate. An oligomer library will typically comprise from about 10 to about 5000 library members, preferably from about lO00 to about 250, 000 library members, and more preferably from about 50,000 to about 10 106 library members .
The labeled synthetic oligomer libraries of the present invention have a wide variety of uses. sy way of example and not limitation, labeled synthetic oligomer libraries can be used to identify peptide, nucleic acid, carbohydrate and/or 15 other structures that bind to proteins, enzymes, antibodies, receptors and the like; identify sequence-specific binding drugs; identify epitopes recognized by antibodies; evaluate a variety of drugs for clinical diagnostic applications; identify materials that exhibit specific properties, such as, for 20 example, ceramics; identify elements comprising superconducting compositions ; combinations of the above,; and other uses that will be apparent to those skilled in the art.
II. Met~ods for Gen~rat;na T,~heled Oliaomer L~hr~ri,~q The present invention also provides methods and apparatus for generating labeled oligomer li~raries. The general methods typically involve synthcc; 7in~ the oligomers in a random combinatorial fashion by a stepwise or concerted series of transformation events. A labeled oligomer library may be produced by synthesizing on each of a plurality of identifier tags linked to a synthesis means (~substrates'~) a single oligomer structure, the oligomer structure being different for - different substrates.
Substrates used for practicing the methods of the present invention include, but are not limited to, an identifier tag SUBSTITUTE SHEET (RULE æ) WO 96/24061 Pcr/uss6101207 2186943 ~ --functionalized with one or a plura~ity of groups or linkers suitable for synthesis; a glass-l~!ir polymer encased identifier tag, which glass or polymer is functionalized with one or a plurality of groups or linkers suitable for synthesis; an identifier tag that is coated with one or a ~lurality of synthesis supports; an identifier tag retained within a frame or housing, which frame or housing is functionalized with one or a plurality of groups or linkers suitable for synthesis; an identifier tag retained within a frame or housing, which frame or housing also retains one or a plurality of plurality of synthesis supports; and the like.
In a preferred embodiment a substrate comprises an~
identifier=tag retained within a frame or housing, which frame or housing also retains one or a plurality of plurality of synthesis supports.
In another preferred embodiment a substrate comprises an identifier tag retained within a frame or housing, which frame or housing is functionalized with one or a pIurality of groups or linkers suitable for synthesis.
In yet another preferFed embodiment a substrate comprises an identifier tag, optionally encased in a glass~or polymeric coating, which identifier tag is functionalized with one or a plurality of groups or linkers suitable for synthesis.
In or~e embodiment of the methods of the present invention a labeled=synthetlc oligomer~ rary is generated that employs ~birth-to-death~ identifier tags. A ~birth-to-death~~
identifier tag is a tag whose informatI:on content does not change during the course of synthesis. P. labeled synthetic oligomer library is synthesize~'in a process~ comprisi~g the steps of: (a) apportioning a plurality of substrates, each of which is pre-encoded with a unique identifier tag (''pre-encoded substrates~) among a plurality of reaction vessels; (b) exposing the pre-encoded substrates in eac~ reactlon vessel to a one or a plurality of transformation events; (c) detecting and recording the identifier tag information from each pre-SUESTITUTE SHEET (RULE 26) WO 96124061 T~ 7 218fi9~3 , 27 encoded substrate in each reaction vessel; (d) apportioning the pre-encoded substrates among a plurality of reaction vessels and (e) repeating steps ~a) through (c) from at least one to about twenty times.
A capping step wherein unreacted functional groups following a transformation event are 'Icapped~' with a highly reactive chemical moiety specific for the functional group(s) desired to be capped may be used after each transformation event, Suitable chemical capping moieties are well known in the art.
Typically, substantially equal numbers of substrates will be apportioned into each reaction vessel. The substrates may be apportioned in a stochastic manner at each step, but preferably will be apportioned in a non-stochastic fashion.
In a preferred embodiment, at least one transformation event is the stepwise or concerted chemical or enzymatic addition of one or a plurality of monomer units.
In an even more preferred embodiment, each transformation event is the stepwise or concerted chemical or enzymatic addition of one or a plurality of monomer units. For this preferred embodiment, a labeled synthetic oligomer library is synthesized in a process comprising the steps of: (a) apportioning a plurality of pre-encoded substrates among a plurality of reaction vessels; (b) exposing the pre-encoded substrates in each reaction vessel to a one or a plurality of monomer units; (c) detecting and recording the identifier tag information from each pre-encoded substrate in each reaction vessel; (d) apportioning the pre-encoded substrates among a plurality of reaction vessels; and (e) repeating steps (a) through (c) from at least one to about twenty times.
A capping step wherein unreacted functional groups following addition of one or a plurality of monomers are '~capped~ with a highly reactive chemical moiety specific for the f~1nr~;rn~l group(s) desired to be capped may be used after each reaction cycle. Suitable chemical capping moieties are SUESTITUTE SHEET (RULE 21~) WO 96/24061 ~ n7 21~6943 `

well known in the art.
As a specific example of=the method, one may consider the synthesis of the set of linear oligomers three monomer residues in length, assembled from a set of four monomers A, B, C, D.
5 See Figure 1. The first monomer is coupled to four different alir,uots of pre-encoded substrates, each different monomer in a different aliry,uot. The identifier information from each pre-encoded substrate is detected and recorded for each different alioLuot. The pre-encoded substrates from all the alio,Luots are 10 then redistributed for a second round of monomer addition.
The pre-encoded substrates may be redistributed in a stochastic fashion. For this method the pre-encoded substrates from all the alir~uots are be pooled, which pool now contains approximately er~ual numbexs of four different types of pre-~
15 encoded substrate~s, each of wh-ich is characteri~ed by the monomer in the first residue position, and redistributed into the separate monomer reaction vessels r~mt;~;n;n~ A, B, C or D
as the monomer. Alternatively, the pre-cncoded substrates may be sorted and redistributed in a non-stochastic fashion into 20 the sepaxate monomer reaction vessels containing A, B, C or D
as the monomer. ~ ~ ~
Following re-distribution a secona monomer: i5 co1lpled and the identifier information from each pre-encoded substrate again detected and recorded for each substrate in each reaction 25 vessel. Each vessel ~ow has substrates with four diiferent monomers in position one and the monomer rnnt;~; n~d in each particular second reaction vessel in position two. The pre-- =~
encoded substrates from all reaction vessels are again~
redistributed among each of the four reaction vessels, and the 30 coupling, detecting and recor~ing ~rocess repeated. The process of sequential coupling and apportioning yields pre-encoded substrates that have passed through all the possible reaction pathways, and the collection of pre-encoded substrates displays all possible trimers -composed of the four I[lonomer 35 inputs A, B, C and D ~3=64 trimers~.
SUBSTITUTE SHEET (RULE 26~

WO 96/24061 PcrluS96/01207 The se~Pnt;~1 detection and recording steps have provided a detailed list of the stepwise monomer additions to which each pre-encoded substrate was subjected ~"reaction histogram~
For example, if the trimer sequence ABC was synthesized on a 5 pre-encoded substrate bearing identifier tag signal "OOl", the recorded reaction histogram would reveal that in the first reaction step substrate OOl was rnnt~; nP~ in the reaction vessel rnnt~;n;n~ monomer A, in the second reaction step substrate OOl was cnnti~;nPd in the reaction vessel rnnt~;n;n~
10 monomer s, and in the third step in the vessel rnnt~;n;n~
monomer C. Thus, detPrm;n;n~ in which reaction vessel a particular pre-encoded substrate was rnntA;nPrl at each reaction step reveals the polymer structure or sequence synthesized on the particular pre-encoded substrate. Thus, it can be 15 appreciated that the ~umber of unique identifier tags needed to label the library is dictated by the number of members in the library being generated.
In another embodiment of the present invention the identifier tags are encoded with information in parallel with 20 generating the oligomer library ~encodable substrates~
The encodable substrates may be pre-encoded with partial identifier lnformation prior to synthesis or may be blank. A
labeled synthetic oligomer library is synthesi~ed in a process comprising the steps of: ~a) apportioning a plurality of 25 encodable substrates among a plurality of reaction vessels; ~b) exposing the su~ostrates in each reaction vessel to one or a plurality of transformation events; ~c) adding identifier information to each identifier tag in each reaction vessel; ~d) apportioning the encodable substrates among a plurality of 30 reaction vessels; and ~e) repeating steps ~a) through ~c) from - at least one to about twenty times.
A capping step wherein unreacted functional groups followIng a transformation event are '~capped' with a highly reactive chemical moiety specific for the functional group~s) 35 desired to be capped may be used after each transformation SUE~STITUTE SHEET (RULE 2r~

WO 96/24061 , ~ /01207 event. Suitable chemical capping moieties are well known in the art.
In a preferred embodiment, at least one tra~sformation event is the stepwise or concerted chemical or enzymatic 5 addition of one or a plurality of monomer units.
In an even more preferred embodiment, each transformation event is the stepwise or concerted chemical or enzymatic addition of one or a plurality of monomer units. For ~this preferred ~mhf~;m~nt, a labeled synthetic oligomer library is 10 synthesized in a process comprising the steps of: (a) apportioning a plurality of encodable substrates among a plurality of reaction vessels; (b) exposing the substrates in each reaction vessel to one or a plurality of units; (c) adding ;~lPnt;~;er i~formation to each idpn~;~;pr tag in~each reaction 15 vessel; (d) apportioning the encodable substrates among a plurality of reaction vessels; and (e) repeating steps (a) through (c) from at least one to about twenty times.
A capping step wherein unreacted functional groups following addition of one or a plurality of monomer units are 20 ~capped~ with a highly reactive chemical moiety specific for:
the functional group(s) desired to be capped may be used after ~ =
each reaction cycle. Suitable :chemical capping moieties are well known in the art.
Typically, substantially e~ual numbers o~ substrates will =
25 be apportioned into each reaction vessel. As discussed,above, the redistribution process may~be stoc~astic, but is preferably =
non-stochastic .
As a specific example of the method, one may again consider the synthesis of the set of oligomers three residues 3 0 in length, assembled from a set of ~ ~i A, B, C, D . See Figure 2. The first monomer is coupled to four different alis~uots of encodable substrates, each different monomer in a different~aliguot. Identifier information is added to =the identifier tags in each ali(Iuotl with the identifier 35 information being unioue for each alitauot. Thus~ each SUBSTITUTE SHEET (RULE 20~

-Wo 96f24061 218 6 9 4 ~ P~7n7 encodable substrate is characterized by the identity of the monomer in the first residue position. The encodable substrates are then redistributed among the separate monomer reaction vessels ~ nt;lin;n~ A, B, C, or D as the monomer.
The second residue is coupled and identifier information unique to each aliquot added to the encodable substrates in each reaction vessel. ,Following this reaction, each vessel now has encodable substrates with four different ~i in position one and the monomer contained in each particular second reaction vessel in position two. The encodable substrates from all reaction vessels are again redistributed among each of the four reaction vessels, the third monomer coupled and ;~1~nt; ~ier information added. The process of sequential re-distributing and coupling yields substrates that have passed through all the possible reaction pathways, and the collection of substrates displays all possible trimers composed of the A, B, C, and D (43=6~ trimers).
Each identifier tag is now labeled with se,quential information that identifies the , 2, to which each encodable substrate was exposed. For example, if one assigned the four monomers A, s, C and D identification labels according to a binary code such that A=00, s=01, C=10 and D=ll, the encodable substrate containing the sequence Asc will contain an identifier tag that reads 000110.
It will be appreciated that the identifier tag ~grows~
with the growing oligomer, and thus the number of unique identification labels, which identification labels uni~uely identify particular transformation events, is dictated by the number of transformation events used to generate the oligomer library. Accordingly, a unique identifier tag is generated for each oligomer in the library by the sequential addition of identification labels identifying the transformation events used to construct the library member.
As will be readily appreciated by those skilled in the art, the method of assembling oligomers from a stepwise or SUeSTlTUTE SHEET (RULE 2~) WO 96/24061 . ~ 7n7 2 1 8 6 9 ~ 3 ~ ¢
concerted series of transformation events can utilize any chemical, physical, enzymatic or biological means, or combinations thereof, that can effect a change in the structure of an oligomer or polymer. The oligomers can be synthesized by introducing, modifying, or removing functional groups or side chains, openlng and/or closing rings, changing stereo chemistry, and the like. Accordingly, the resulting oligomers can be linear, branched, cyclic, or assume various other conformations that will be apparent to those of ordinary skill in the art . .~eP f igures 3, 4, 5 and 6 .
In addition, because the substrates are app~ortioned amongst a number of reaction vessels, transformation events using different physical chemical, enzymatic or biologlcal chemistries, or combination thereof can be used to assemble the oligomers. Examples of the plethora of transformation events that can be used with the present invention are described in, for example, application ~erial No. 08/180, 863 filed Jan. 13, 1994, which is~assigned to the assignee of th'e present ~
invention and PCT Publication WO 94/08057 entitled, "Complex Combinatorial J.ibraries Encoded with Tagsii April 14 (1994~, each of which is incorporated herein by re~erence.
Thus, those skilled in the~art will appreciate that the methods of the present invention can be used to synthesize labeled libraries of virtually any chemic'al composition including, but not lïmltea to, '~a--miaes, ~ estërs, thloethers, ketones, ethers, sulfoxides, sulfonamides, sulfones, phosphates, alcohols, aldehydes, alkenes,' alkynes, aromatics, polyaromatics, heterocyclic compounds containing= one or~ more of the atoms of: nitrogen, sulfur, oxygen, and phosphorous, and the like; chemical entities having a common core structure such as, for example, terpenes, steroids, ,B-lactams, benzodiaze~lnes, xanthates, indoles, indolones, lactones, lactams, hydantoins, ~linnnPC, hyaro~uinones, and the like;
chains of repeating monomer units such as polysaccharides, SU~STITUTE SHEET ~RULE 26) Wo96124061 r~~ L.~01207 IE186~43 phospholipids, polyurethanes, polyesters, polycarbonates, poly ureas, polyamides, polyethyl,~n~ir;n~q, poly arylene sulfides, polyimides, polyacetates, polypeptides, polynucleotides, and the like; or other oligomers or polymers as will be readily 5 apparent to those skilled in the art.
In a preferred embodiment, at least one transformation event ir, the generation of a labeled synthetic oligomer library is the stepwise or concerted enzymatic or chemical addition of one or a plurality of r~r q, In another preferred embodiment, each transformation event in the generation of a labeled synthetic oligomer library is the stepwise or concerted enzymatic or chemical addition of one or a plurality of ~
In these preferred modes, the functionalities connecting 15 monomers need not be identical. Thus, polymers composed of non-identical interlinkages are ~ nt~ ted by the preferred embodiments. Also contemplated are oligomers that are composed of non-uniform monomer composition. As one example, an oligomer may be composed of aryl or alkyl hydroxyl, aryl or 20 alkyl carboxylic acid, and aryl or alkyl amine ~ a. As another example, an oligomer may be composed of deoxyribonucleoside, carbohydrate, and amino acid monomer units .
Although typically the present invention will utilize 25 solid phase synthesis strategies, the present invention also contemplates solution phase chemistries. Techniques for solid phase synthesis of peptides are described, for example, in Atherton and Sheppard, Solid Ph;3qe Pe~t;de Svntl~oqis: A
Practical An~roach, IRL Press at Oxford University Press, 30 Oxford, England (1989); for oligonucleotides in, for example, Gait, Oli~onucleotiae Svnt~qis. A Practical ~nr~roach, IRL
Press at Oxford University Press, o~ford, England (1984); each of which is incorporated herein by referencG.
Techniques for solution and solid phase multiple Gomponent SUBSTITUTE SHEET (RULE 26) Wo96/24061 PCrlUS96101207 2186943 i`;~

combinatorial array syntheses strategies include U,S. Patent Application No. 08/092,862 filed Jan~13, 1994, which is assigned to the assignee of the present invention, and which is incorporated herein by ref erence .
Other synthetic strategies ~that may be employed by the present invention are described in, for example, Bunin et al., "The Combinatorial Synthesis and Chemical and Biological Evaluatio~ of a 1,4-senzodiazepine Library, ~ Proc. ~t1, Acad.
~ 91:4708-12 (1994) and U.S. Patent No. 5,288,514, entitled "Solid Phase and Combinatorial Synthesis of Benzodiazepine Compounds~on a Solid Support,~ issued Feb. 22, 1994; and Chen ~L, "`Analogous' Organic Synthesis of Compound Libraries:
Validation of Combinatorial Chemistry in Small-Molecule Synthesis, ~' J . Am, c~m . Soc . 1 1 6: 2661-2662 ~1994~
Thus, as those of skill in~t~e art will appreciate, the methods of the present invention may be used with virtually any synthesis strategy, be it chemical, biological or otherwise, that is now known or will be later developed, to generate libraries of oligomers or polymers. ~ -The representation of çach library member within the library depends on apportioning the substrates into the proper reaction vessels at each reaction cycle in the synthesis series. In one embodiment the substrates can be pooled at each step, mixed a~d stochastically re-apportioned into reaction vessels i~or subses[uent reaction~ cycles . For stochastic mixing and apportioning, increasing the number of substrates upon which a single oligomer se~luencç will be synthesized increases the likelihood that each oligomer sequence will be represented in the 1 ibrary .
In a ~referred embodiment the substrates ar~e apportioned in a non-stochastic manner at each reaction cycle. Non-stochastic distribution has two distinct advantages. Flrst, it ensures that each oligomer se~uence is represented in the synthesis library, even if only a single substrate is employed SUBSTITUTE SHEET (RU~E 26) WO 96~061 ;~ ~ ~ 6 ~ 4 3 ~ I ~,lIL.,_ ;;1`171~7 for each oligomer sequence. Second, it increases the 1 ;kr~l ih~od that all oligomer sequences are represented in subs~n~ ly equal quantities in a synthesized library.
The non-stochastic redistribution process at each reaction 5 cycle will be dictated by the composition of the library.
Generally, the composition of any library can be descri~ed as a series of sequential matrix calculations. The number of different transformation events at each synthesis cycle is represented by a horizontal ~chemical input~ matrix. T~e 10 composition of the library at the begin~ing of each cycle is defined by a ~library matrix~. The composition of the library at the completion of any cycle is the product of the library matrix ( from the beginning of the cycle~ and the chemical input matrix for the cycle ~ust completed.
The matrix notation can be best illustrated by way of specific example. If one desires to construct the complete set of linear oligomer trimers composed of four different monomer inputs A, B, C, and D (43=64 library members), the chemical input matrix at each cycle is [A, B, C, D]. Thus, at the end 20 of the first monomer addition step, -t~le library matrix is the vertical matrix , where the subscript denotes the -AB-25 reaction cycle number in th~ series of synthesis reaction cycles .
The composition of the library following the second round of transformation events ~here monomer addition reactions) is obtained by taking the product of the chemical input matrix for 30 cycle two and the library matrix from cycle one. Here, the composition of the library at the end of the second reaction cycle is given by:

B BA BC BB BD
~A, B, C, D]2X C = CA CC CB CD
SUEISTITUTE SHEET (RULE 26) .. . . . .

WO96/24061 ~ ;, r~.,~ n7 3 6 ~
~-The composition of the complete set of trimers ~ i . e . at the end of the third reaction cycle) is given by:
AAA ACA ABA ADA AAB ACB ABB ADB
BAA BCA BBA BDA BAB BCB BBB BDB
CAA CCA CBA CDA CAB CCB CBB CDB
AA AC AB AD DAA DCA DBA DDA DAB DCB DBB DDB
0 [A, B, C, D] 3 X BA BC BB BD = AAC ACC ABC ADC AAD ACD ABD ADD
DA DC DB DD BAC BCC BBC BDC BAD BCD BBD BDD
CAC CCC CBC CDC CAD CCD CBD CDD
DAC DCC DBC DDC DAD DCD DBD DDD

This matrix notation illustrates the redistribution 15 process that must take place at each reaction cycle to generate a library of a particular composition. Specifically, at each reaction cycle each set of. substrates in a particular reaction vessel must be divided into subsets, where the number of subsets is ec~ual to the number of different transformation 20 events at that cycle. The exact distribution process will depend on the composition of the library, and will be rRadily apparent to those skilled in the art upon review of this disclosure. ~ =
In one preferred embodiment the substrates can be manually 25 sorted and reapportioned at each reaction cycle. This can be illustrated by way of specific example for a library comprising the complete set of NXn oligomers composed of xr monomer inputs assembled in N reaction cycles. For the first monomer addition reaction NXr' substrates are divided into xn reaction vessels, 30 NXn/Xr substrates per vessel. Integer multioles of NX :~
substrates may also be used. After addition of the first monomer inputs Xl, X~, . . . xn, the substrates in each of the x vessels are divided into Xn ali~uots and reapportioned into the xr vessels, one ali~uot per vessel. Following the second 3 5 reaction cycle each library member can be represented as NXr .X, , SUBSTITUTE SHEET (RULE 26) WO 96124061 21 8 6 9 4 3 ~ n7 where X~.l represents the first monomer added to the substrate and Xr7 represents the second monomer added to the substrate.
For the third monomer addition step, each subset of substrates ~X~,lX"2 is divided into Xn aliquots and reapportioned 5 into the X" reaction vessels, one aliQuot per vessel.
Repeating this process N times generates the complete set of oligomers comprised of Xn monomer inputs.
Modifications of this exemplary approach are also possible. For example, one may use any series of 10 transformation events at any reaction cycle. The set of transformation events may be f~n~lP~l or contracted from cycle to cycle; or the set of transformation events could be changed completely for the next cycle (e.g. couple a monomer in one cycle, rearrange stereochemistry in another cycle).
15 Additionally, one can fix certain transformation events at some cycles while varying other transformation events, to construct oligomer F~ J~'JLl~S wherein certain residues or regions within oligomers are altered to provide diversity.
In another preferred embodiment the substrates are sorted 20 and re-apportioned at each cycle using automated sorting eQuipment. Substrates are placed in a mechanical hopper which introduces them into a vibratory sorter apparatus such as are commonly employed in the manufacturing industry to sort small objects. The vibratory sorter introduces the substrates one at 25 a time into a delivery chute. Attached to the chute is a detector which can scan the identifier tag and receive a uni~ue identifier code. When the code is received the substrate is released from the chute and drops into a reaction vessel. A
conveyor system may be used to position one of a series of 30 reaction vessels under the sorter chute for receipt of the substrate. After the ~ i er tag has been read the conveyor system may then be positioned such that the correct reaction vessel is positioned under the chute to sort individually or in groups as desired.
SUBSTITUTE SHEET (RULE 26) WO 96/24061 A ~ n7 2186943 - ~
~ ',Ij . ! ~.t:
38 ~ '-~
.i. .
. IrlPnt; fvin thP Se~uPnce of Anv-~liqnmPr The present invention provides methods for identifying the structure of any of the oligomers in the library. By tracking the synthesis pathway that each oligomer has taken, one can deduce the sequence of any oligomer in a given library. The method involves linking an identifier tag to an oligomer that indicates the series of transfrr~t-rn events, and corresponding synthesis cycles in which those transformation events were experienced, that an oligomer has experienced during construction of a labelea synthetic oligomer library.
In one embodiment~ after a series of synthesis cycles and concurrent identifier tag ~PtPrt;rnq, one tracks the transformation events to which a particular identifier ~tag, and thus oligomer, was subjected at~ each synthesis cycle to determine the oligomer structur~e. In another embodiment, after a series of synthetic cycles and concurrent identifier=tag additions, one ~reads~ the identifier tag associated wlth an oligomer to determine the structure of the particular oligomer.
The ;~lPnt;f;Pr tags therefore identify each transformation event that an individual oligomer library member has experienced. In addition, a record of the synthesis cycle in the synthesis series at which each transformation even~t was experienced is generated ( ~reaction histogram~ ) . As dèscribed above, the identifier tags may be pre-encoded with unique identifier information prior to= synthesis, or can be encoded with information lmmediately before, during, or~after each transformation event. Methods employing pre-encoded identifier tags, and thus wherein a unique identifier tag is assigned to each library member prior to synthesis, require a number of unique i~Pnt; f; Pr tags equal to the number of library mem'oers .
Methods employing Pnro~hl e identifier tags and wherein identifier information is added at each transformation.event require only as many unique ;~lPnt;f;cation labels, which labels uniquely ident'fy particular t~ansfrr~-t;rn events, as there SUBSTITUTE SHEET ~ULE ~) WO 96/24061 PCr/US96/01207 2186~43 are different transformation events in the synthesis cycle.
Unique identifier tags identifying the structure of each oligomer in the library are generated concomitant with synthesis as identification labels identifying each 5 transformation event are added, preferably in a sequential fashion, to the encodable identifier tags at each synthesis cycle. In this latter embodiment the identifier tags preserve a sequential record of which particular transformation events a substrate experienced at each synthesis cycle.
. Tvmeq of IdPnt; fier Ta~s The identifier tags of the insta.nt invention may be any detectable feature that permits elucidation of the structure of each oligomer synthesized in a given labeled library. Thus, 15 identifier tags may be, for example: microscopically distinguishable in shape, size, color, optical density, etc differentially absorbing or emitting of light; chemically reactive; pre-encoded with optical, magnetic or electronic information; or in some other way distinctively marked with the 20 required decipherable information.
In a preferred embodiment of the invention, the identifier tags relate information back to a detector when pulsed with electromagnetic radiation.
In a more preferrea embodiment the identifier tags are 25 microchips that are either pre-encoded or encodable with a uni~ue radiofrequency "fingerprint~ that can be detected by pulsing the identifier tag with electromagnetic radiation.
The radiofrequency fingerprint may be a single radiofrequency band, or a combination of radiofrequency bands.
30 When pulsed with ele.:L, I ~nF~tic radiation, the identifier tags emit a radiofrequency fingerprint that is detected by an electromagnetic radiation detector. ~herefore it can be appreciated that the number of unique radiofrequency identifier tags, or ~fingerprints,~ that are available is virtually 35 limitless.
SUESTITUTE SHEET (RULE 26) WO 96/24061 I ~ A t ~,A,7 21869~3 .`` - --40 ~
The ;~ nt;~;er tags of the present invention can be pre-encoded with unigue identifier: information prior to synthesis of a labeled synthetic oligomer~ library. For example, an identifier tag may be a bar code strip that corresponds to, 5 say, the number OOI, or it may be a radiofres~uency fingerprint comprised of one or a plurality of frequency bands. ' Each library member is thus labeled with a unigue, static identifier tag throughout the combinatorial synthesis, or in a ~'birth-to-death~ fashion. ~
The identifier tags may aIso be encodable with new information from time to time. For example, the identifier tag may be a bar code stri~ that can receive sequential in~ormation from time to time or a microchip that can be ~downloaded~ with digital information from time to time. The .~n~oflAhl e 15 identifier tags may be either blank or pre-encoaed with partial or complete identifier information prior to=~ synthesis of a labeled synthetic oligomer library.
Each transformation event in a series of reaction cycles in the synthesis of a labeled syntXetic oligomer library'is 20 assigned a unique identification label, which label is added to ' the encodable identifier tag either concomitant with, or close in time to, performance of a particular transformation'event.
At the termination of a synthesis comprising an unlimited number of~ reaction cycles and transformation events, a unique 25 sequential signal has been downl n~ l onto the microchip such that the history of transformation events to which the ~
encodable substrate was subjected is recorded in a sequential fashion on the microchip. The oligomer se~uence~ can therefore be deduced by detecting the unique se~uential identification 30 information t-nnt~;nFrl in the identifier tag.
In another preferred embodiment the identifier tags of the present invention are encased in a glass or polymeric material.
Such glass or pplymeric material may be readily attacfied to-synthesis supports, directly derivatized with one or a~
35 plurality of functional groups suitable for synthesis, or SU~STITUTE SHEET (RULE 26~

~wo 96/24061 2 1 8 6 9 4 3 P IIL ,1~.'01207 directly derivatizea with one or a plurality of linkers bearing one or a plurality of functional yroups suitable for synthesis.
It can be readily appreciated that the identity of such functional groups will be dictated by the composition of the desired oligomers. Suitable groups will be readlly apparent to those skilled in the art and include, but are not restricted to, amino, carboxyl, sulfhydryl, hydroxyl, and the like.
Any glass or polymeric material capable of encasing an identifier tag can be used in the present invention. In one mode such polymeric material is capable of being derivatized with one or a plurality of functional groups or linkers suitable for synthesis. Polymers such as polyethylene glycol polystyrene-divinyl benzene, polyethylene grafted polystyrene, polyacrylamide-kieselguhr composites and glass have all been commercialized with functional groups suitable for derivatization with various linkers and monomers. Methods for derivatizing such polymers are well known in the art. See, e.g., Atherton and Sheppard, Solid Ph~e Pe~tide Svnthesi~: A
Practic~l ~nmroach~ IRL Press at Oxford University Press, Oxford, England (1989), and Gait, Oliqonucleotide Svnthesis: A
Practic~l Annroach, IRL Press at Oxford University Press, Oxford, Englana (1984), each of which is incorporated herein by reference.
Suitable preferred identifier tags are well known in the art and are described, for example, in U.S. Patent No.
5,252,962, entitled ~System Monitoring Programmable Implantable Transponder,~ issued on Oct. 12, 1993, to sio Medic Data Systems, Inc. and U.S. Patent No. 5,351,052, entitled IlTransponder System for Automatic Identification Purposes,"
issued on Sept. 27, 1994, to Texas Instruments, Inc., each of which is incorporated herein by reference. Commercially available examples include ELAMSlM (Electronic Laboratory Animal Monitoring Systems), manufactured by siomedic Data Systems, 225 West Spring Valley Ave., Maywood, NJ 07607, and SuasTlTuTE SHEET (RULE 2~

W0 961A061 , ~ 1(`1?n7 21869~ ~
42 .~
TIRISTM (Texas Instruments ~egistratio~iand Identification Sy6tem), manufactured by Texas Instruments, 12501 Research Blvd., Mailstop 2243, Austin, TX 78759.
ELAMS~, which are widely used to tag and identify 5 laboratory mice via subcutaneous injection of the ELA~, comprise glass-encased microchips that are pre-tuned to emit a unique radiofrequency fingerprint when pulsed with electromagnetic radiation. TIRIS~M, which are currently used for security cards and to track~ and identify livestock and 10 automobiles, comprise glass-encased microchips that can be downloaded with digital information from time to time.
ELAMSTM and TIRISTM possess a variety of features that make them ideally suited for use as combinatorial chemistry library ~r~Pntlf;er tags. For example, ELAMSTM and TIRISTM can be 15 readily sorted using currently available automated sorter technology. In addition, the encoded information can be scanned and stored in a microcomputer. Furthermore, ELAMS~M
and TIRISTM are compatible with virtually any chemist~y now known or that will be later developed to generate olilJomer or 20 polymer libraries. Thus, large labeled libraries of virtually any chemical composition can be generated in an automated fashion, there'oy increasing the diversity of labeled libraries available while decreasing the time and effort necessary to generate such libraries. :

SUBSTITUTE SHEET (RULE 26) ~WO 96/24061 2 1 8 6 9 4 3 , ~ "01207 ..

V. T,;nkinq t~P ol;rnmprs to t~P IdentifiPr Tars An oligomer of the present invention may be linked to an itlPnt;f;Pr tag in a variety of fashions. ~, for example, Figure 7. One or a plurality of oIigomers of identical 5 ser~uence can he attached directly to one or a plurality of functional groups on an identifier tag, to one or a plurality of linkers that are attached to an identifier tag, or to one or a plurality of synthesis supports that are attached to an identifier tag. An identifier tag may also be retained within 10 a frame or housing to which one or a plurality of oligomers of identical structure are attached. Additionally, an identifier tag may be retained within a frame Qr housing that also retains one or a plurality of synthesis supports having attached thereto one or a plurality of oligomers of identical structure.
In one preferred embodiment one or a plurality of oligomers of identical structure are attached directly to one or a plurality of i~lnctional groups on an identifier tag.
Typically, the identifier tag will be encased in a glass or polymeric material that ca~ be derivatized with one or a 20 plurality of functional groups suitable for synthesis. Any polymeric material capable of providing functional groups suitable for attachment can be utilized. It can be readily appreciated that the identity of the functional groups will be dictated by the composition of the desired oligomers. Suitable 25 groups will be readily apparent to those skilled in the art and include, but are not limited to, amino sulfhydryl, hydroxyl, and the like.
Several polymeric materials have been commercialized with suitable functional groups such as, for example, polystyrene-30 divinyl benzene, polyethylene yrafted polystyrene,polyacrylamide kieselguhr composite and controlled pore glass.
Methods for derivatizing such polymers are well known in the art. See, e.g., Atherton and Sheppard, Solid Ph~qe Pe~tide Synthesis: A Pract; c;~l An~roar~, IRL Press at Oxford SUBSTITUTE SHEET (RULE 2~) WO 961Z4061 ~. 1, 1 i r ~ ^ ?(17 218694~

University Press, Oxford, England ~(1989), and ~ait, Oliann~ l eoti~lP Svnth~is: A Practical ~n~roach, IRL Press at:
Oxford UnLversity Press, Oxford; England (1984), each of which is incorporated herein by, reference.
Alternatively, one or a plurality of oligomers of identical structure may be attached to the functional groups 4n an identifier tag by means of a_linker. A linker is generally a moiety, molecule, or group of ;molecules attached to a synthesis support or substrate and spacing a synthesized polymer or oligomer from a synthesis support or substrate.
Typically a linker will be bi-functional, wherein said linker has a functional group at one end capable of attaching to a monomer, oligomer, synthesis support or substrate, a series of spacer residues, and a functional group at another end capable of attaching tQ a monomer, oligomer, ~=synthesis support or substrate.
The functional groups of a bifunctional linker need not be identical, thereby allowing the linker to act as a ~functional group adapter. ~ Thus, ~ifunctional linkers provide a means whereby the functional ~roup displayed on a substrate or synthesis support, say an amino group, can be converted into a different functional group, say a hydroxy~ group. The~use of bifunctional linkers can therefore greatly increase the repertoire of chemistries that can take a~dvantage of solid phase synthesis strategies.
The composition and length of the linker will depend in large part upon the application of the library. The degree of binding between an immobilized library me~ber and its binding partner may in some embodiments depend on the accessibility of 3 0 the i hi 1 1 zed lLbrary member to its binding partner . ~ The accessibility in turn may depend on the length and/or chemical composition of the linker moiety.
The composition ~of the linker moiety will also depend on the desired properties of the linker, and in large ~art will be dictated by the physical conditions and~or biological or SUBSTITUTE SHEET (RULE 26) Wo 96/24061 PCrlUSs6l01207 ~ 2186943 .

chemical reagents to which the linker will be exposed during synthesis. For example, one may desire a rigid linker, such as for example, poly-proline or poly-allyl, or one may desire a flexible linker such as, for example polyalanine or saturated 5 hydrocarbons.
It is desirable that the linker be stable to the reaction conditions used to construct the library. Linkers of suitable composition will be readily apparent to those skilled in the art, or may be later developed.
The number of spacer residues that comprise the linker may also vary. Typically, a linker will generally comprise about 1-100 spacer residues, preferably about 1-20 spacer residues, and usually about 5-15 spacer residues.
Spacer residues may be atoms capable of forming at least two covalent bonds, such as carbon, silicon, oxygen, nitroyen, sulfur, phosphorous, and the like. Spacer residues may also be molecules capable of forming at least two covalent bonds such as amino acids, nucleosides, nucleotides, sugars, aromatic rings, hydrocarbon rings, carbohydrates, branched or linear hydrocarbons, and the like. Thus, the interlinkages comprising the linker include, but are not limited to, amides, ethers, esters, ureas, phosphoesters, thioesters, thioethers, and the like. The interlinkages connecting spacer residues may be, but need not be, identical.
Linked together, the spacer residues may form linear, cyclic, branched, or other types of structures. Thus, a linker may provide a plurality of functional groups to which oligomers may be attached, thereby increasing the quantity of oligomer synthesized. Linked together the spacer residues may be rigid, semi-rigid or :flexible. The spacer~residues comprising the linker may be, but need not be, identical.
Such linker moieties may be capable of later releasing the synthesized molecules by some specific, regulatable r^chAn i sm .
Such regulatable merh~n; cmq include but are not restricted to thermal, photochemical, electrochemical, acid, base, oxidative SUEISTITUTE SHEET (RULE 26) WO 96/24061 ~ 207 ~18~943 and reductive reactions . Several linkers- which provide a variety of functional group coupling and cleavage strategies are commercially available.
As will be readily apparent to the skilled artisan upon review of this disclosure, the labeled combinatorial synthesis methods and apparatus described herein can be used to ootimize linker composition and length.
In another preferred embodiment, one or a plurality of oligomer of identical structure may be attached to one or a 0 plurality of synthesis supports that are attached to an~
identifier tag. An oligomer may be covalently attached directly to a functional group on the synthesis support, or may be attached: to a synthesis support by means of a linker as described above. In one preferred embodiment one or a~
plurality of synthesis supports: are attached to an identifier tag by physical means such as glue or magnetic attraction.
Virtually any physical means that is stable to the reaction conditions employed to syn~hf~Rl ze the library may be used.
In another preferred embodiment, one or a plurality of synthesis supports is covalently attached to an identifier tag ~optionally encased in a glass or~polymeric~ coating) . Such covalent attachment can be either directly to one or :a =
plurality of functional groups Qn the identifier tag, or by means of a linker as described above. ~ ~
In yet another preferred~ embodiment an identifier tag may be retai~ed within a frame or housing, which frame or~housing also retains one or a plurality of oligomers of identical structure or one or a plurality of synthesis supports having attached thereto one or a plurality of oligomers of identical structure Such oligomer attac~ment may~be either directly to a functional group on the synthesis support, or may be mediated by a linker as described above.~
In still another preferred embodiment an identifier tag may be retained in a frame or housing, which frame or housing has attached ther~eto one. or a plurality of oligomers of SUESTITUTE SHEET (RULE 26) WO 96124061 ~ '01207 ~ 21 ~ 6 g ~ 3 !, . . .

identical structure. Such oligomer attachment may be either directly to a functional group on the frame or housing, or may be mediated by a linker as described above.

VI. Fnrr,d;n~T t~e Id~ntifier Ta~ In~-rr~-tion A variety of types of information may be encoded on the identifier tags of the present invention. For example, the identifier tags may be pre-encoded with a bar code strip, 10 moieties which differentially absorb or emit light, magnetic or optical information, or any o~her uniquely identifiable and detectable mark. Thus, the means employed for encoding the identifier tag information is dictated by the means employed for detecting the encoded identification signal.
In a preferred embodiment, an identifier tag comprises a microchip that is imprinted with a unis[ue radiofrequency ~ fingerprint~ that is transmitted back to a detector when the identifier tag is pulsed with electromagnetic radiation. In this embodiment, a microchip is exposed to a beam comprising 20 one or a plurality of radiofrequency bands. The microchip draws power from the beam. The microchip has an electronic fingerprint. Thus, microchips of different fingerprints will emit different signals when pulsed with electromagnetic radiation. Accordingly, each of a plurality of microchips can 25 be pre-encodea with a unique '~fingerprint~ or identification label. The skilled artisan will appreciate that the number of microchips that can be imprinted with a unique identification label is virtually without limit. Such microchips are well known in the art, and are described in, for example, U.S.
Patent No. 5,148,404, entitled ~lTr~ncp~nrl~r and Method for the Production Thereof, ~ issued on Sept. 15, 1992, to Texas Instruments, Inc., and which is incorporated herein by reference .
In another preferred embodiment an identifier tag 35 comprises a microchip that can be imprinted with digital or SUE~STITUTE SHEET (RULE 26~

Wo 96/24061 . ~l/. '01207 ,, j, ., sequential information at each reaction cycle in a series of reaction cycles. The identifier tag can be either pre-encoded with partial or complete identifier information or blank prior to synthesis of a labeled synthetic oligomer libr-ary. ~~
Concomitant with, or at a point close in time to, each reaction cycle a new multi-digit identifying the transformation event a partisular .onro~hl e substrate experiencea is downl ni~lr~ to the identifier tag such that a history of transformation events to which the ;rl~nt;~;er tag was subjected is resorded. Since the identifier information at each cycle is added se~uentially to the microchip, each oligomer structure can be elucidated by detecting the sequential digital information contained in the identifier~ tag linked to that particular oligomer~ Suitable digitally encodable substrates and encoding me-thods are well known or will be apparent to those skilled i~ the art, and are described in, for example U.S.~Patent No. 5,351,052, entitled "Transponder=Systems for Automatlc Identification Purposes,'l issued on Sept. 27, 1994 to Texas Instruments, Inc and U.S.
Patent No. 5,252,962, entitled ''3ystem Monitoring Pro~L ~: hle Implantable Transporlder, rl issued~ on Oct. 12, 1993, to Bio Medic Data Systems, Inc., each of which is incorporated herein by ref erence .
VII. R~roverinr~ ;3n~1 Decotl;nr t7~ ntifier Tar~ Inforr-tion When specific library members are isolated in a receptor screening experiment, the substrates can be segregated :~
individually by a nurber of means, including:
micrnm~n;r~ tion, magnetic attraction, sorting, or fluorescence activated cell sorting (FACSJ, although with 3 0 respect to the present invention FACS is more accurately '~fluorescence activated oligomer sorting.U See MPtl~ndq in Cell gy, Vol 33, Darzynkiewicz, Z. and Crissman, ~. A. eds., Academic Press; and Dangl and Herzenberg~ r lnnl Met~orl~
52:1-1~ (1982~, both of which are incorporated herein by SUESTITUTE SHEET (RULE 26~

Wo 96/2406~ 01207 218fi943 49 re f erence .
Once the desired substrates have been isolated, the identity of the ;f~f~nt;fier tag must be ascertained to obtain the structure of the oligomer on the substrate. The method of 5 identification will depend on the type of identifier tag used to encode the library. For example, bar code ;r~pnt;fier tags can be scanned with laser devices commonly employed in the art to read bar codes. Fluorescent identifier tags can be read by obtaining a fluorescence spectrum.
In preferred embodiments employing microc~ip identifier tags, the ;d,=nt;f;er tag information can be read using detectio~ devices commonly employed in the art to scan and store identifier information from such tags. Typically such detectors 'can scan, display, transmit and store identifier 15 information received from an identifier tag. Such detectors are well ~cnown in the art and are described, for example, in U.S. Patent No. 5,262,772, entitled ~Transponder Scanner~
issued Nov. 16, 1993, to Bio Medic Data Systems, Inc., which is incorporated herein by reference. Such systems that read, 20 display, transmit and store identifier information and that can be interfaced with a microcomputer are commercially available, including Bio Medic Data Systems models DAS-4004EM, DAS-40020A
and DAS-4001.
In preferred 'lo~;m~nts~ the detection system employed 25 will be interfacea with a computer to automate identifier tag information storage. In even more preferred embodiments the detection equipment will be interfaced with a computer and automated sorting equipment.
30 VIII. Scre~n;nq Rece~tors with L;~l-eled Svnthetic Oliqomer Libr~rie~
The labeled synthetic oligomer libraries of the present - invention wlll have a wide variety of uses. By way of example 35 and not limitation, labeled synthetlc oligomer libraries can be used to identify peptide, nucleic acid, carbohydrate and/or SUBSTITUTE SHEE~ (RULE 26~

WO 96/24061 r~ 7n7 2186g43 " '', 5 ~
other structures that bind to protei~s; enzynies, antibodies, receptors and the like; identify se~uencè:specific binding drugs; identify epitopes recogn=ized by antibodies; evaluate a variety of drugs for t l ;n;--~l diagnostic applications; identify 5 materials that exhibit specific properties, such as, for example, ceramics; identify elements comprising superconducting compositions; combinations of the above; and other uses that will be apparent to those skilled in the art.
synthetic oligomers displayed on substrates can be 10 screened for the ability to bind to a receptor. The receptor may be contacted with the library of synthetic oligomers, f orming a bound member between a receptor and the oligomer capable of binding the receptor. ~ The bound member may then be identified. As one example, the receptor may be an antibody.
The techni~ues for selection of individual substrates displaying ligands on their surface are analogous to FACS
methods for cloning ~ cells expressing cell surface antigens and receptors. Therefore, methods for selecting and sorting substrates will be readily a~parent to those skilled in 20 the art of cell sorting. For example, a receptor ~can be labelled with a fluorescent tag and then incubated with the mixture of substrates displaying the oligomers. After ~ashing away un-bound and non-specifical~y bound receptors, one can then use FACS to sort the beads and to identiy and isolate 25 physically individual beads show~ing high fluorescence. ~ :
Alternatively, if the physical size o the substrates permits, one can manually identify and sort the substrates showing high fluorescence.
Alternatively, the present invention can be used to 3a generate llbraries o~ soluble labeled oligomers, which can be used with a variety of screening methods. For instance, The substrates can be sorted and placed in individual compartments or wells, such as, for exampIe, the wells of a 96-well microtitre plate. The oligomers are cleaved from the 35 substrates and l~ ~;nf~rl contained wlthin the well along with SUBSJITUTE SHEET (RULE 2~

Wo 96124061 r~ n7 2186943 ~. ~
.; . .

the ~ nti~ier:tag. ~ The library members may then be assayed in solution by a variety of techniques that will be readily ~pparent to those skilled in the art of immunology, one example of which is described below.
In one '~ ';~~ t the bottom surface of each well is coated with the receptor. After addition of the binding buffer and a known ligand for that receptor that is fluorescently labelled, one effectively has a solution phase competitive assay for novel ligands of the receptor. The binding of the 10 fluorescently labelled ligand to the receptor is estimated by confocal imaging of the monolayer of immobilized receptor.
Wells showing decreased fluorescence on the receptor surface indicate that the released oligomer competes with the labelled ligand. The substrates in the wells showing competition are 15 recovered, and the identifier tag decoded to reveal the sequence of the oligomer.

SUESTITUTE SHEET (RULE 26) Wo 96/24061 ~ J,. /01207 2i86~43 . SYNTHESIS OF ONE-HUNDRED AMIDES
One hundred unique i~Pnti f;P~ tags containing Rink polymer are subdivided into ten groups of ten, and each group of ten is introduced into a separate 250 mL reaction vessel charged with 100 mL of methanol solvent. To each reaction vessel is then added 10 1nL of a solution r~nt~;n;n~ an aldehyde dissolved in methanol, a different aldehyde added to each reaction vessel.
TXe reaction is stirred for six hrs at room temperature, or until completion of the reaction. The reaction may be monitored using standard techniques for the monitoring of solid phase reactions. After completion of the reaction, the solvent and excess reagents are removed from each of the ten reaction vessels independently, and the polymer in each vessel washed three times with methanol and dichloromethane and allowed to dry using reduced pressure.
The unique identif ier tags are then recorded by removing the contents of each reaction vessel and passing the uni~ue identifier tag by a detector ~Che unique identifier tag~ for each oIigomer is thus recorded ~id cross-r fèrence-d to the reaction vessel from which it was removed.
The unique identifier tags associated with the Rink~
polymer are then randomly recombined and again subdivided into ten groups of ten, and each group of ten placed into a different reaction vessels (250 mL) r~nt~;n;ng 100 mL dichloromethane.
Each of the ten reaction vessels:is charged with base, and ten unique acid chlorides ~are introduced into the reaction vessels, one acid chloride per vessel.
The reactions are allowed to proceed to completion_ The~
reactions may be monitored using-standard methods. After completion, the solvent is removed by filtration and the oligomer~in each reaction vessel_is washed independently with three washes each of methanoI ana dichIoromethane. Eac~ of the ten identifier tags is then removed from each vessel and passed 3 5 by a detector to record their unlque ide~tif ication numbers .
SUBSTITUTE SHEET (RULE 26) WO 96/24061 2 ~ 4 ~ 01Z07 Thus, each identification number is associated with a specific reagent utilized in the first step of the synthesis (an aldehyde) and the second step of the synthesis ~an acid chloride), providing a unique "reaction histogram~ for each of the one hundred unique identif ier tags .
After completion of the reactions, the identifier tags associated with each polymer are separately deblocked using trifluoroacetic acid and introduced into a microtiter plate such that each well of the microtiter plate contains only a single polymer. After removal of solvent and evaporation to dryness, each well contains a unique structure.
The decoding of said structure can be accomplished by comparing the individual identifier tag with histogram for that particular tag. That is, the i~1~nt;f;Pr tag will be associated with a specific structure for the aldehyde monomer input and a specific structure for the acid chloride monomer input. The structure of the polymer f nn~; n~ in each well is thus known uneguivocally .
X. ~YN'l'lll!;SlS ON- ELAMSIM OF FOUR PENTAPEPTIDES
A. Derivatizati on of ET,~.M~
Four (or multiples thereof ) ELAMSTM (Biomedic Data Systems), each having a unioue identifier tag are washed with r~fl~;n~ agueous HNO3 for 20 min. The ELAMS~M are pelleted and washed with distilled water (5x) and methanol (3x) and dried at 125C for about 12 hours. The ELAMS~ are then vortexed in with a solution of 5~ (v/v) aminopropyltriethoxysilane in acetone for ten hours, washed with acetone ( 2x), ethanol ( 5x) and methylene chloride (2x) and dried at 125C for 45 min.
The EI.AMS~ are suspended in anhydrous DMF (1 mL) cnn~;nin~ diisopropylethylaminè (DIEA) (17 mL, 100 mmoles) and a solution of Fmoc-b-alanine pentafluorophenyl ester (200 mg, 420 mmoles, Peninsula Labs) in distilled water (1.5 mL) added.
After treatment with shaking for about 12 hours the ELAMSrM can SUBSTITUTE SHEET (RULE 26) Wo 96/24061 2 1 8 6 9 4 3 ~ ~ 7n7 be collected and washed with ~F (3x) and; mëthylene chloride ~2x). ELA~qs~M are treated with a solution of 109~i acetic anhydride in DMF rn~nt~in;nr 0.05 mol of 4-dimethylaminopyridine to cap uncoupled aminopropyl groups and then washed with DMF
5 (2x) and methylene chloride (2x). ELAMS~ are then vortexed with a solution of 209~ piperidire in DMF to release the Fmoc protecting group. The Fmoc-piperidine adduct can be quantitated by monitoring the ;~hsr,rh~nrP spectrum of the superratant at 302 nm (e30,=7800 ~ cm~l) to estimate the degree of substitution of 10 amino groups per qaantity of E. Einally, the ELAMSrM are washed with ethanol (5x) and methylene chloride (2x) and dried at 85CC
for about 12 hours.
B . Prer~rat; on of Boc-Glv-L-Phe-L-Leu-OH
Glycyl-L-phenylalanyl-L-leucine (552 mg, 1.5 mmol, Bachem) is dissolved in a solution containing distilled water ~10 mL) and 1 M NaOH (1.5 mL). The solution is cooled in An ice~bath and treated with a solution of dL-tert-butyl pyrorArhnn;~P t337 mg, 1. 5 mmol) in p-dioxane tl2 mL) . The solution is stLrred f~r 20 4 hours at room temperature, after which the solution is concentrated to dryness in varllo, the residue taken up in water (5 mL) and the pH adjusted to 2.5 by the addition of 1 M=KHSOs.
The aqueous suspension ls extracted with ethyl acetate 12x, 15 mL), the organic layer separated and dried over magnesium 25 sulfate. After removal of the solvent ;n y;~rllo the residue can be titurated with hexane to yield Bor-Gly-L-Phe-L-Leu-OH as a white solid ~
Prel~ration of Glv-L-Phe-L-Leu ~,~MC:lM
soc-Gly-L-Phe-L-Leu-OH (~44 mg, 0.1 mmol), benzotriazol-1-yloxytris(dimethylamino)r~rsr~r~n;l~m hexaflurophsophate (14 mg, 0.104 mmol) are dLssolved in dry DMF ll mL). DIEA (20 mL, 0.115 mmol) is added and about 0.5-1.0~mL of this solution is SUBSTITUTE SHEET (RULE 25) WO 96/24061 J ~I/~J~ L ~ n7 2~8fi943 transferr~d to a test tube containing amino derivatized ELAMSTM.
The tube ls sealed, vortexed for about 3 . 5-4 hours and the ELAMS~d pelleted and washed with DMF (3x) and methylene chloride (2x). The ELAMS~M are then deprotected with a solution of 50 trifluoroacetic acid (TFA) in methylene chloride for 30 min., washed with methylene chloride (2x), ethanol (2x) and methylene chloride (2x), and dried at 55C for about 1 hour. The identifier tag from each ELAMS~ is detected and recorded.
D- Prer~rat;on of Glv-Glv-L-Phe-L-Leu ~SEO In NO:5) ET~M~TM
Fmoc-glycine pentafluorophenyl ester (46 mg, 0.1 mmol) is dissolved in anhydrous DMF (1 mL) o~nti~;nin~ DIEA (17 mL, 0.1 mmol). About 0.5-1.0 mL of this solution is added to Gly-L-Phe-L-Leu ELAMS~ in a test tube and the tul~e vortexed for about 3 hours. The ELAMSTM are pelleted and washed with DMF (4x~ and methylene chloride (2x). Deprotection can be effected by treatment with a solution of 2096 piperidine in DMF for 30 min.
The ELAMSTM are then washed with DMF (2x), ethanol (2x) and methylene chloride (2x) and-dried at 60C for 4 hours. The identifier tag for each ELAMS~M is detected and recorded.
E. Preoaration of L-Pro-Glv-L-Phe-L-Leu (SEO ID No:6) T~T,~
Fmoc-L-proline pentafluorophenyl ester (50 mg, 0.1 mmol) is dissolved in anhydrous DMF (1 mL) oont~ining DIEA (17 mL, 0.1 mmol). About 0.5-1.0 mL of this solution is added to Gly-L-Phe-L-Leu ELAMS~{ in a test tube and the tube vortexed for about 3 hours. The ELAMSTM are pelleted and washed wiT,h DMF (4x) and methylene chloride (2x). Deprotection can be effected ~y 30 treatment with a solution of 20~ piperidine in DMF for 30 min.
The ELAMSTM are then washed with DMF (2x), ethanol (2x) and methylene chloride (2x) and dried at 60C for 4 hours. The identifier tag for each EI.AMSlM is detected and recorded.
SUBSTITUTE SHEET (RULE 26) WO 96124061 i~ 01207 F. PrPr~ra~ion of Tvr-Gly-Glv-L-Phe-L-Leu tSE~ Tn NO: 1) antl Tvr-Pro-Glv-L-Phe-L-Leu (SEO In NO:2) ET,AM~IM
Fmoc-O-t-butyl-L-tyrosine pentafluorophenyl ester (63 mg, 5 0.1 mmol) is dissolved in anhydrous DMF (1 mL~ containing DIEA
(17 mL, O.l~mmol). About 0.5-1.0 mL of this solution is added to Gly-Gly-L-Phe-L-Leu (SEQ ID NO:5) and Pro-Gly-L-Phe-L-Leu (SEQ ID No:6) ELAMSlM in a test 'tube and the tube vortexed for about 3 hours The ELAMSTM are pelleted and washed with DMF
10 (4x) and methylene chloride (2x). Deprotection can be effected by treatment with a solution of 20% piperidine in DMF for 30 min, followed by treatment with a solution of 5096 ~FA in methylene chloride for 30 min. The ELAMSTM are then washed with DMF (2x), ethanol (2x) and methylene chloride (2x) and dried at 15 60C for 4 hours. The i~lDnrif;r~r tag for each ELAMS~M is detected and recorded.
G. Prer~ration of Pro-L-Pro-Glv-L-Phe-L-~eu (SEO ID NO.'3) An~l Pro-Glv-Glv-L-Phe-L-Leu (SEO ID NO:4) ET,~M~lM
2 0 . = _ _ Fmoc=L-proline penta~Eluorophenyl ester (50 mg' 0.1 mmol) is dissolved in anhydrous DMF (1 mL) cnntA;ninr DIEA (17 mL, 0.1 mmr,l). About 0.5-1.0 mL of t~iS solution is added~to Gly-Gly-L-phe-L-Leu ISEQ ID NO:5) and Pro-Gly-L-Phe-L-Leu (SEQ ID NO:6) 25 ELAMSlM in a test tube and the tube vortexed ~or about 3 hours.
The ELAMS~M are pelleted and washed with DMF (4x) and methylene chloride (2x) . Deprotection ca~ be effected by treatment with a solution of 20% piperidi~e in DMF for 30 min. The ELAMSlM are then washed with DMF (2x), ethanol (2x) a~a methylene chloride' 30 (2x) and dried at 60C for 4 hours. The identifier tag for each ELAMSTM is ~l~t~rt~ and recorded EI. SPlect;on of ET,~ M ContA;n;nr PeRtide Liq~nflc for MrnrClon;~1 Antihodv 3E7 Monoclonal antibody 3E7 can be raised against opioid peptide beta-endorphin. The binding specificity of MAb 3E7 has SUBSTITUTE SHEET (RULE 26~

WO 96124061 2 1 8 6 9 4 3 ~ P~ r~n7 ;
been well characterized by solution assays with chemically synthesized peptides. The eauilibrium bindiny constants ~Kd) of the peptides considered here are as follows: YGGFL (SEQ ID
NO:1) is 6.6 n~; and YPG~L (SEQ ID NO: 2), PPGFL (SEQ ID NO:3), 5 and PGGFL (SEQ ID No:4) are each >1 mM; thus, only peptide YGGFL
(SEQ ID NO: 1~ shows appreciable a~finity for the antibody.
A mixture of ELAMSTM rr,nt~;n;n~ either YGGFL ~SEQ ID NO:1), YPGFL (SEQ ID No:2~, PGGFL (SEQ ID NO:4), or PPGFL (SEQ ID NO:3) are added to phosphate buffered saline (PBS) containing 10 monoclonal antibody 3E7 that has been previously conjugated to colloidal superparamagnetic microbeads (Miltenyi Biotec, West Germany). After a 16 hour incubation at 4C, beads which bind the 3E7 antibody can be selected using a high strength magnet.
The ;~lpnt;L;er information of the selected beads is then analyzed with a model DAS-4001EM or DAS-4001 detector (Bio Medic Data Sys tems ) . Analys is wi ll reveal tha t only ELAMSTM upon which YGGFL (SEQ ID NO:1) was synthesi~ed are selected by the 3E7 antibody.
Alternatively, the ELAMSTM can be ;nr~lh~tP~ with 3E7 20 antibody that has been previously conjugated with a fluorophore such as fluorescein or rhodamine, and peptide-antibody binding detected with a fluorimeter or epifluorescence microscope using the appropriate wavelength of light 25 XI . PARALr EL SYNTHESIS OF ~hJ~'l'll~hS ON ELAMSIM
A. DPrivat;zina A~;nn Er.~r~TM wit~ a L;nkPr ELAMS~M containing amino groups and each having a uniaue identifier tag are prepared as described in Example II.A., above. The ELAMS~M are treated with a mixture of 4-Fmoc-30 aminobutyric acid N-hydroxysucr;nlrr;r~P ester (1 mmol), HBTU (1 mmol), HOBt (1 mmol) and DIEA (1 mmol) in ~:1 methylene chloride:DMF (10 mL). After vortex treatment for 30 minutes, the reaction mixture is diluted with DMF (10 mL), the ELAMSTM
pelleted, and the supernatant decanted. The ELAMS~M are washed 35 with D~qF ( 3 x lû mL). The coupling procedure may be repeated SUBSTITUTE SHEET (RULE 26) 218 6 9 ~ 3 ~ n7 t '~

with fresh rea~ents and the ELAMS~M pelleted and~ washed as described above. , ,`Y~
g. pAr;:ll 1 el Svn~h~sis of Peoti~s The parallel assembly of linear oligomers is shown schematically in Figures 1 and 2. The general method for parallel assembly of polypeptides can be illustrated by way of specific example. Twenty linker-derivatized ELAMSIM, each having a unigue identifier tag ~Example III.A. ) are placed in a reaction vessel and the segue~ce GGFL (SEQ ID NO:5) synthesized on each of the twenty ELAMSTM using standard Fmoc peptide synthesis reagents and chemistry as described in Atherton &
Sheppard, Solid Ph~e Peotide Svnthesis: A Practic;3l P~roach, IP~L Press, Oxford, England (1989).
Following removal of the Fmoc groups by treatment with 3096 piperidine in DMF for 60 min., the ELAMSlM are then apportioned into twenty reaction vessels, one ELAMT~ per vessel. Each vessel is then charged with a 5~ t;n)n ~-~ntA;n;n3 an amino acid monomer ( O .1 M), HsT~7 ( O .1 M), Host ( O .1 M) and DIEA ( O .1 M) in 9:1 methylene chloride:DMF for 30=~min., a dif~erent amino acid monomer per vessel. The coupling may be repeated with fresh reagents for=a further 30 min. The ELAMSTM are then washed with DMF (3x) and then with acetonitrile (3x). The identifier tag information is detected and recorded for each ELAMSTU in each reaction vessel, along with the identity of the monomer added.
Side chain protecting groups are~removed using standard deprotection chemistry. ~iÇ~ Atherton & Sheppard, Solid Ph~se Pe~;de Svnthesis: A Practical l~,nDroach. IF~L Pres~, Oxford, England (1989), and the library assayed as described in Example II.F.
For libraries with larger diversity, successive rounds of coupling and identifier tag scanning and recDrding can be performed.
SUBSTITIJTE SHEET ~RULE 26) WO 96/24061 ~ ~ P~ n7 XII. PAPALLEL ~YN~ S OF O~IGONUCLEOTIDE OCTAMERS
A. Pron~rat;on of HYtlr~llVl ET,~.~IM
Sixteen ELAMSTM, or multiples thereof, each having a uni~ue identifier tag are cleaned in concentrated NaOH, followed by 5 exhaustive rinsing in water. The ELAMS~M are derivatized for 2 hr with a solution of 1096 (v/v~ bis (2-hydroxYethyl) aminopropyltriethoxysilane (Petrarch Chemicals, Bristol, PA) in 9596 ethanol, rinsed thoroughly with ethanol (2x) and ether (2x), dried ~ n vacuo at 40C, and heated at 100C for 10 15 min.
B . Pren~ration of ~ nker A synthesis linker, 4, 4-dimethoxytrityl-hexaethyloxy-b-cyanoethyl phosphoramidite, can be prepared using 1, 6-15 dihydroxyhexane as starting material according to the method of Beaucage and Caruthers, Atkinson and Smith, "Solid Phase Synthesis of Oligodeoxyribnucleotides by the Phosphite-Triester Method,~ Gait, Oli~onllcleotide Svnt~qis: A Practi~l AnT~roach, IRL Press, Oxford, England (1984) using 2-cyanoethyl 20 N,N-diisopropylchlorophosphoramidite (Sigma, St. Louis, MO~ as the phosphitylating reagent.
C. Att~c~r^nt of SYnt~ is T,1nk~r Synthesis linkers can be attached to ELAMSTM by reacting 25 hydroxylated ELAMS~M (described in Example IV.A., above) with

4, 4-dimethoxytrityl-hexaethyloxy-b-cyanoethyl phosphoramidite using standard phosphoramidite chemistry as described in Gait, Oliaonucleotide svnth~ : A Practical Anoroac71, IRL Press, Oxford, England (1984). Typical reaction conditions are 0.1 M
30 phosphoramidite, 0 . 25 M tetrazole in anhydrous acetonitrile for 1-3 min. The ELAMSlU are rinsed with acetonitrile (3x).
Following (-n~lpl; n~, any unreacted hydroxyl groups can be capped if desired. ELAMSTM are added to fresh capping solution SUESTITUTE SHEET (RULE 26~

Wo 96124061 r~ 01207 2186g43 ."'`~ ~' ~ . r 60 ~ ` ' which is prepared as follows: 3 volu~nes of a solution of 6.5%
(w/v) 4-dimethylaminopyridi~e (DMAP) in anhydrous tetrahydrofuran (THF) are mixed with l volume of a solution of 40% (v/v) acetic anhydride in 2, 6-lutidine. The reaction is

5 allowed to proceed for 1-3 min., after which the ELAMSTM are =
rinsed with methylene chloride (2x) and acetonitrile (3x).
After capping, the phosphite triester bond is r~ li zPci to a phosphotriester by treating the ELAMSlM with 0 . lM iodine solution prepared by dissolving 2 . 6 g iodine in a mixture containing 80 mL THF, 20 mL 2, 6-l~utidine and 2 mL water for about l min. The ELAMS~ are rinsed with acetonitrile until the effluent is colorless.
The dimethoxytrityl groups protecting the hydroxyls~ can be removed by treatment with 2% (v/v) dichloroacetic acid (DCA) in 15 methylene chloride for about l min. followed by rinsing (3x) with methyIene chloride. The number of hydroxyl groups per E~ AMSTM ~ i . e . the loading capacity) can be determined by taking the absorbance of the dimethoxy trityl cation ~ff~ nt at 498 nm (e49e=14,300 M~l cm~l).

D . Pr~n~ration of Fluoresceinvl ~ted Probe A tar~et probe of sequence 5'-GCGCGGGC-fluorescein can be prepared using 3 ~ -Amine-ONlM control pore glass (CPG) (Clontech, Palo Alto, CA) and standard DNA synthesis reagents ~Applied 25 8iosystems, Foster City, CA) . The 3 ' -amine can be labeled with fluorescein isothiocyanate to generate a 3 ~ -fluorescein labeled oligomer according to the manufacturer ' 5 instructions supplied with 3 '-Amine-ON~M CPG.
30 E. p~r;lllel Svnt~cis of Octanucleotides Target oligomer sequences, represented by the matrix 3 ~ -CGC (A+T+C+G) 2CCG can be prepared by synthesizing on each of sixteen linker-derivatized ELAMSrM, each having a~unique identifier tag (described in Example IIV.C. ) :polynucleotide SUBSTITUTE SHEET ~RULE 2~

- - ~
WO 96/24061 ~ nt7~7 sequence 3 ' -CGC using standard base-labile DNA synthesis reayents and chemistry ~Applied Blosystems, Foster City, CA).
Following the r~lllr1; n~ cycle, the ELAMSTM are distributed into four reaction vessels, four ELAMS~ per vessel. A single 5 nucleotide monomer (as the protected phosphoramidite) is coupled to the ELAMSTM in each reaction vessel using standard base-labile DNA synthesis reagents and chemistry, a different nucleotide monomer per vessel, and the capping, oxidation, and DMT removal steps completed.
The identifier tag from each ELAMSTM in each reaction vessel is detected and recorded using, for example, a model DAS-4001EM or model DAS-4001 scanner ~Bio Medic Data Systems, Maywood, NJ), along with the identity of each monomer added in each vessel. The ELAMSTM are then distributed by placing one 15 ELAMSTM from each current reaction vessel into each of four new reaction vessels, and a second nucleotide monomer added as described above, a different monomer per vessel. The identifier information is detected and recorded for each ELAMSTM in each reaction vessel, along with the identify of the monomer added in 2 0 each vessel .
The ELAMSTM are then pooled into a sinyle reaction vessel and the sequence 3-CCG added to eash ELAMSTM using standard DNA
synthesis reagents and chemistry. The exocyclic amine protecting groups are removed by treatment with conc. ammonia 25 according to the manufacturer ' s instrllction for base-labile nucleotide phosphoramidites.
XIII. ~ U~ ; SPECIFIC TARGET HYBRIDIZATION
The deprotected ELAMS~M are incubated with the 30 fluoresceinylated probe under conditions conducive to ser~uence specific hybridization as described in Hames and Higgins, Nucleic Arid Hvbridizat;on: A Pract;c;~l Ar-r)roar~, IRL Press, Oxford, England (1985) . Following rinse cycles the ELAMS~M can be interrogated for hybridization using a fluorimeter or 35 epifluorescence microscope (488-nm argon ion exci~ation). The SUBSTITUTE SHEET (RULE 26) WO 96124061 ~ ! . `'1/~ ~01207 21~6g~3 . ~;
62 ~
ELAMSlM displaying the highest photon counts are isolatea and the identifier tag scanned and compared to the reaction histogram for that particular ide~ntifier tag, revealing that the setauence 3 ~ r~f~c~2c~ was synthesized on t~e ELAM~ dispIaying 5 the highest photon count.
While the invention of this patent application is disclosed by reference to specific examples, it is understood that the present invention can be applied to all chemistries lO that are amenable to combinatorial strategies and to alI
identifier tags that relate information to a detector when pulsed with electr~ nPtic radiation. Further, the present invention is intended to be ~rr~ hl e to all future developed solid phase and muIti-~ ~ ^nt comhinatorial array syntXeses, 15 and to all future irlpnt;fler tags that relate information to a detector when pulsed with electromagnetic information.
Accordingly, the invention may be embodied in other~
specific forms without departing from its spirit or essential characteristics. It is to be understood that this disclosure is 20 ;ntpn~pd in an illustrative rather than a llmlting sense,~ as it is contemplated that modificatio~s will readily occur to those skilled in the art, within ~e spirit--of t~e invention and the scope of the appended claims.

SUBSTITUTE SHEET (RULE 26 r~ n7 WO ~6124061 2 1 8 6 9 4 3 63 SEQUENCE LISTING J
(1~ GENERAL lN1 U~ ~ JN:
(i) APPLICAI~: Cargill, John Armstrong, Robert W.
(ii) TITLE OF INVENTION: METHOPS AND APPARATUS FOR 81w~ lN~i L~3ELED COMBIN~.TORIAL C~EM}STRY T.
(iii) NUMBER OP ::i~u~wc~.:,: 6 (iV) ~:Jk~UNlJ~Nt_/:; ADDRESS:
A ~ ~nnRFAqFF: Pennie and Edmonds B STREET: 1155 Avenue of the Americas C CITY: Ne~ York D STATE: Ne~.r York ~E COUNTRY: U S.A~
F~ ZIP: 10036 (v1 COM2UTER READABLE FORM:
, A MEDIUM TYPE: Floppy disk B COMPUTER: IBM PC compatible C~ OPERATING SYSTEM: PC-DOS/MS-DOS
~Dl SOFTWARE: PatentIn Release #1.0, Version #1.25 (vi~ CURRENT APPLICATION DAT~:
(A) APPLICATION ~UMBER: US To be assigned.
(B) FILING DATE: O1-FEB-1995 (C; CLASSIFICATION:
(viii) ATTORNEY/AGEUT INFORMATION:
(A) NAME: Halluin, Albert P.
(B) I~ NUMBER: 25,227 (C) kEr~u:w~:/DOCRET N~MBER. 8140-009 (ix) TEL~ . INFORMATIOU:
(A) TFT~T~p~rJN~ 415--854-3660 (B) TELEFAX: 415-854-369q (C) TELEX: 66141 PENNIE
(2) INPORMATION FOR SEQ ID NO:l:
(i) SEQ~ENCE 'IT~R~'T~RTRTICS:
A LENGT~: S amino acids B ~ TYPE: amino acid C: sTR~NnFn~R.~R unknown D TOPOLOGY: unknown (ii) MO~ECULE TYPE: peptide (xi) SEQUENCE DESCRIP~ION: SEQ ID NO:l:
Tyr Gly Gly Phe Leu SUBSTITUTE SHEET (RULE 26) 218 fi 9 4 3 , ~ 6~ n~
WO 96/24061 64 ' ' 12) INFORMATION FOR SEQ ID NO:2:
(i) SEQUENCE CHARACTERISTICS: .
A LENGTH: S amino acids B1 TYPE: amino acid : ;-C STRr~ nN~qC: unknown .' 1:D 1 TOPOLQGY: unknown (ii) MOLECULE TYPE: peptide (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:
yr Pro Gly Phe Leu (2) INFORMATION FOR SEQ ID NO:3:
(i~ SEQ'JENCE ~ `T~TCTICS:
A ~ LENGT~: S amino acids B ~ TYPE: amino acid C ~ STR~.J~ 55: unknown D 1 TOPOLQGY: unknown (ii) MOLECULE TYPE: peptide ~=
(xi~ SEQUENCE DESCRIPTION: SEQ ID NO:3:
ro Pro Gly Phe Leu ~2~ INFQRMATION FOR SEQ ID NO:4:
~i~ SEQ'dENCE ~ TFl~TcTIcs:
,A LENGTB: s amino acids B: TYPE: amino acid ,C~ ST~ J~ S: unknown D, TOPOLOaY: unknown (ii~ MOLECULE TYPE: peptide (Xi~ SEQUENCE DESCRIPTION: SEQ ID NO:4:
ro Gly Gly Phe Leu (2~ INFORMATION FOR SEQ ID NO:S:
(i) SEQUENCE CHARACTERISTICS:
IA LENGTH: 4 amino acids B TYPE: amino acid C STRANDEDNESS: unknown D 1 TOPOLQGY: unknown ~ii) MOLECULE TYPE: peptide SU~STITUTE SHEET (RULE 26) WO 96/24061 2 1 8 ~ 9 4 3 65 ~ PCTIUS96101207 txi) SEQUENCE Llh:~-,Kl~llU~: SEQ ID NO:S:
Gly Gly Phe LeU
(2) INFORMPTION FOR SEQ ID NO:6:
( i ) SEQUENCE ~IDT~ D~
LENGTH: 4 an~ino acids ~3 TYPE: alnino acid C. sT~ n'~c~: unknown D I TOPOLOGY: unknown (ii) MOL.ECULE TYPE: peptide ~xi) SEQUENCE ~Jh':,~'Kl~l.lUN: SEQ ID NO:6:
~ro G y Phe Leu SUBSTITUTE SHEEf ~F(ULE ~6)

Claims (53)

WHAT IS CLAIMED IS:

1. A labeled synthetic oligomer library comprising a plurality of different members, each member comprising an oligomer linked to an identifier tag identifying the structure of said oligomer.

2. The library of claim 1, wherein said linkage between said oligomer and said identifier tag comprises a synthesis support.

3. The library of claim 1, wherein said linkage between said oligomer and said identifier tag comprises a linker between said identifier tag and said synthesis support and a linker between said synthesis support and said oligomer.

4. The library of claim 1, wherein said linkage between said oligomer and said identifier tag comprises a linker between said oligomer and said identifier tag.

5. The library of claim 1 wherein said identifier tag is attached to said oligomer.

6. The library of claim 1 wherein said identifier tag is retained within a frame or housing and said oligomer is attached to a synthesis support, which synthesis support is also retained within said frame or housing.

7. The library of claim 1 that has from about 100 to about 250,000 members.

8. The library of claim 1, wherein said oligomers are structurally related analogues having a common core structure.

9. The library of claim 1 wherein said oligomers are selected from the group consisting of: benzodiazepine, b-lactam, hydantoin, quinone, hydroquinone, terpene, carbohydrate, polypeptide and polynucleotide.

10. The library of claim 1 wherein said identifier tag relates information back to a detector when pulsed with electromagnetic radiation.

11. The library of claim 10 wherein said identifier tag is selected from the group consisting of: encodable microchip and pre-encoded microchip.

12. The library of claim 11 wherein said encodable microchip is a TIRISTM and said pre-encoded microchip is an ELAMTM.

13. The library of claim 1 wherein:
the library has from about 100 to about 250,000 members;
said oligomers are structurally related analogues having a common core structure; and the identifier tag is selected from the group consisting of: pre-encoded microchip and encodable microchip.

14. A labeled synthetic oligomer library produced by synthesizing on each of a plurality of pre-encoded substrates, each of which has a unique identifier tag, a single oligomer structure comprising the steps of:
a) apportioning said pre-encoded substrates among a plurality of reaction vessels;
b) exposing said pre-encoded substrates in each reaction vessel to one or a plurality of transformation events;

c) detecting and recording identifier information for each of said identifier tags in each of said reaction vessels;
d) apportioning said pre-encoded substrates among a plurality of reaction vessels; and e) repeating steps a) through c) from at least one to about twenty times.

15. The library of claim 14, wherein said oligomer is attached to a synthesis support and said pre-encoded substrate comprises a frame or housing retaining said identifier tag and said oligomer.

16. The library of claim 14, wherein at least one transformation event is a stepwise or concerted enzymatic or chemical addition of one or a plurality of monomers.

17. The library of claim 14, wherein said oligomers are structurally related analogues having a common core structure.

18. The library of claim 14, wherein said oligomers are selected from the group consisting of: benzodiazepine, b-lactam, hydantoin, quinone, hydroquinone, terpene, carbohydrate, polypeptide and polynucleotide.

19. The library of claim 14, wherein said oligomer is cleaved from said pre-encoded substrate after completion of oligomer synthesis.

20. A labeled synthetic oligomer library produced by synthesizing on each of a plurality of encodable substrates a single oligomer structure comprising the steps of:
a) apportioning said encodable substrates among a plurality of reaction vessels;

b) exposing said encodable substrates in each reaction vessel to one or a plurality of transformation events;
c) adding identifier information to said encodable substrates;
d) apportioning said encodable substrates among a plurality of reaction vessels; and e) repeating steps a) through c) from at least one to about twenty times.

21.The library of claim 20, wherein said oligomer is attached to a synthesis support and said pre-encoded substrate comprises a frame or housing retaining said identifier tag and said oligomer.

22.The library of claim 20, wherein at least one transformation event is a stepwise or concerted enzymatic or chemical addition of one or a plurality of monomers.

23.The library of claim 20, wherein said oligomers are structurally related analogues having a common core structure.

24. The library of claim 20, wherein said oligomers are selected from the group consisting of: benzodiazepine, b-lactam, hydantoin, quinone, hydroquinone, terpene, carbohydrate, polypeptide and polynucleotide.

25. The library of claim 20, wherein said oligomer is cleaved from said pre-encoded substrate after completion of oligomer synthesis.

26. The library of claim 20, wherein said encodable substrate is blank prior to synthesis of a labeled oligomer library, and wherein each transformation event in a series of transformation events in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with each transformation event.

27. The library of claim 20, wherein said encodable substrate is encoded with a partial identifier information prior to synthesis, and wherein each transformation event in a series of transformation events in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with each transformation event.

28. A method of preparing a labelled synthetic oligomer library comprising a plurality of different members, each member comprising a pre-encoded substrate linked to a single oligomer structure and bearing a unique identifier tag identifying said oligomer structure, said method comprising the steps of:
a) apportioning said pre-encoded substrates among a plurality of reaction vessels;
b) exposing said pre-encoded substrates in each reaction vessel to one or a plurality of transformation events;
c) detecting and recording identifier information for each of said identifier tags in each of said reaction vessels;
d) apportioning said pre-encoded substrates among a plurality of reaction vessels; and e) repeating steps a) through c) from at least one to about twenty times.

29. A method of preparing a labeled synthetic oligomer library comprising a plurality of different members, each member comprising an encodable substrate linked to a single oligomer structure and having a unique identifier tag identifying said oligomer structure, said method comprising the steps of:
a) apportioning said encodable substrates among a plurality of reaction vessels;
b) exposing said encodable substrates in each reaction vessels to one or a plurality of transformation events;
c) adding first identifier information to said encodable substrates;
d) apportioning said encodable substrates among a plurality of reaction vessels; and e) repeating steps a) through c) from at least one to about twenty times.

30. The method of claim 28 wherein said encodable substrate is blank prior to synthesis of a labeled oligomer library, and wherein each transformation event in a series of transformation events in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with each transformation event.

31. The method of claim 29, wherein said encodable substrate is encoded with a partial identifier information prior to synthesis, and wherein each transformation event in a series of transformation events in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with each transformation event.

32. The method of claim 29, wherein said encodable substrate is an encodable microchip.

33. The method of claim 28, wherein said pre-encoded substrate is a pre-encoded microchip.

34. A labeled synthetic oligomer library produced by synthesizing on each of a plurality of pre-encoded substrates, each of which has a unique identifier tag, a single oligomer structure comprising the steps of:
a) apportioning said pre-encoded substrates among a plurality of reaction vessels;
b) exposing said pre-encoded substrates in each reaction vessel to one or a plurality of monomers;
c) detecting and recording identifier information for each of said identifier tags in each of said reaction vessels;
d) apportioning said pre-encoded substrates among a plurality of reaction vessels; and e) repeating steps: a) through c) from at least one to about twenty times.

35. The library of claim 34, wherein said oligomer is attached to a synthesis support and said pre-encoded substrate comprises a frame or housing retaining said identifier tag and said oligomer.

36. The library of claim 34, wherein said oligomers are formed by the concerted addition of one or a plurality of monomers.

37. The library of claim 34, wherein said oligomers are structurally related analogues having a common core structure.

33. The library of claim 34, wherein said oligomers are selected from the group consisting of: benzodiazepine, b lactam, hydantoin, quinone, hydroquinone, terpene, carbohydrate, polypeptide and polynucleotide.

39. The library of claim 44, wherein said oligomer is cleaved from said pre-encoded substrate after completion of oligomer synthesis.

40. A labeled synthetic oligomer library produced by synthesizing on each of a plurality of encodable substrates a single oligomer structure comprising the steps of:
a) apportioning said encodable substrates among a plurality of reaction vessels;
b) exposing said encodable e substrates in each reaction vessel to one or a plurality of monomers c) adding identifier information to said encodable substrates;
d) apportioning said encodable substrates among a plurality of reaction vessels; and e) repeating steps a) through c) from at least one to about twenty times.

41. The library of claim 40, wherein said oligomer is attached to a synthesis support and said pre-encoded substrate comprises a frame or housing retaining said identifier tag and said oligomer.

42. The library of claim 40, wherein said oligomers are formed by the concerted addition of one or a plurality of monomers.

43. The library of claim 40, wherein said oligomers are structurally related analogues having a common core structure.

44. The library of claim 40, wherein said oligomers are selected from the group consisting of: benzodiazepine, b-lactam, hydantoin, quinone, hydroquinone, terpene, carbohydrate, polypeptide and polynucleotide.

45. The library of claim 40, wherein said oligomer is cleaved from said pre-encoded substrate after completion of oligomer synthesis.

46. The library of claim 40, wherein said encodable substrate is blank prior to synthesis of a labeled oligomer library, and wherein each step in a series of oligomer monomer additions in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with the addition of monomers.

47. The library of claim 40, wherein said encodable substrate is encoded with a partial identifier information prior to synthesis, and wherein each step in a series of oligomer monomer additions in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with the addition monomers.

48. A method of preparing a labelled synthetic oligomer library comprising a plurality of different members, each member comprising a pre-encoded substrate linked to a single oligomer structure and bearing a unique identifier tag identifying said oligomer structure, said method comprising the steps of:
a) apportioning said pre-encoded substrates among a plurality of reaction vessels;
b) exposing said pre-encoded substrates in each reaction vessel to one or a plurality of monomers;
c) detecting and recording identifier information for each of said identifier tags in each of said reaction vessels;
d) apportioning said pre-encoded substrates among a plurality of reaction vessels; and e) repeating steps a) through c) from at least one to about twenty times.

49. A method of preparing a labeled synthetic oligomer library comprising a plurality of different members, each member comprising an encodable substrate linked to a single oligomer structure and having a unique identifier tag identifying said oligomer structure, said method comprising the steps of:
a) apportioning said encodable substrates among a plurality of reaction vessels;
b) exposing said encodable substrates in each reaction vessels to one or a plurality of monomers;
c) adding first identifier information to said encodable substrates;
d) apportioning said encodable substrates among a plurality of reaction vessels; and e) repeating steps a) through c) from at least one to about twenty times.

50. The method of claim 49 wherein said encodable substrate is blank prior to synthesis of a labeled oligomer library, and wherein each step in a sequence of oligomer monomer additions in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with the addition of each monomer.

51. The method of claim 49, wherein said encodable substrate is encoded with a partial identifier information prior to synthesis, and wherein each step in a sequence of oligomer monomer additions in the synthesis of a labeled oligomer library is recorded by adding identifier information to said encodable substrate in conjunction with the addition of each monomer.

52. The method of claim 48, wherein said pre-encoded substrate is a pre-encoded microchip.

53. The method of claim 49, wherein said encodable substrate is an encodable microchip.