WO2000001711A1 - Reusable solid support for oligonucleotide synthesis - Google Patents
Reusable solid support for oligonucleotide synthesis Download PDFInfo
- Publication number
- WO2000001711A1 WO2000001711A1 PCT/CA1999/000600 CA9900600W WO0001711A1 WO 2000001711 A1 WO2000001711 A1 WO 2000001711A1 CA 9900600 W CA9900600 W CA 9900600W WO 0001711 A1 WO0001711 A1 WO 0001711A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- group
- linker arm
- unsubstituted
- substituted
- moiety
- Prior art date
Links
- 239000007787 solid Substances 0.000 title claims abstract description 32
- 238000002515 oligonucleotide synthesis Methods 0.000 title claims abstract description 25
- 125000005647 linker group Chemical group 0.000 claims abstract description 201
- 238000000034 method Methods 0.000 claims abstract description 103
- 239000002777 nucleoside Substances 0.000 claims abstract description 32
- -1 methoxyacetyl Chemical group 0.000 claims description 176
- 230000008569 process Effects 0.000 claims description 96
- 229910052739 hydrogen Inorganic materials 0.000 claims description 61
- 239000001257 hydrogen Substances 0.000 claims description 61
- 125000002877 alkyl aryl group Chemical group 0.000 claims description 51
- 125000003118 aryl group Chemical group 0.000 claims description 51
- 108091034117 Oligonucleotide Proteins 0.000 claims description 50
- 125000002887 hydroxy group Chemical group [H]O* 0.000 claims description 45
- 150000002431 hydrogen Chemical class 0.000 claims description 40
- 125000006239 protecting group Chemical group 0.000 claims description 35
- VHYFNPMBLIVWCW-UHFFFAOYSA-N 4-Dimethylaminopyridine Chemical compound CN(C)C1=CC=NC=C1 VHYFNPMBLIVWCW-UHFFFAOYSA-N 0.000 claims description 28
- 150000001875 compounds Chemical class 0.000 claims description 25
- 150000003833 nucleoside derivatives Chemical class 0.000 claims description 25
- 239000000126 substance Substances 0.000 claims description 20
- 239000003795 chemical substances by application Substances 0.000 claims description 17
- MCTWTZJPVLRJOU-UHFFFAOYSA-N 1-methyl-1H-imidazole Chemical compound CN1C=CN=C1 MCTWTZJPVLRJOU-UHFFFAOYSA-N 0.000 claims description 16
- 125000000217 alkyl group Chemical group 0.000 claims description 16
- 125000004435 hydrogen atom Chemical group [H]* 0.000 claims description 16
- 239000000203 mixture Substances 0.000 claims description 16
- 150000004820 halides Chemical class 0.000 claims description 15
- VYPSYNLAJGMNEJ-UHFFFAOYSA-N Silicium dioxide Chemical compound O=[Si]=O VYPSYNLAJGMNEJ-UHFFFAOYSA-N 0.000 claims description 13
- NIXOWILDQLNWCW-UHFFFAOYSA-M acrylate group Chemical group C(C=C)(=O)[O-] NIXOWILDQLNWCW-UHFFFAOYSA-M 0.000 claims description 12
- 230000003213 activating effect Effects 0.000 claims description 12
- 125000003545 alkoxy group Chemical group 0.000 claims description 12
- 125000004185 ester group Chemical group 0.000 claims description 12
- 150000002148 esters Chemical class 0.000 claims description 11
- 125000002221 trityl group Chemical group [H]C1=C([H])C([H])=C([H])C([H])=C1C([*])(C1=C(C(=C(C(=C1[H])[H])[H])[H])[H])C1=C([H])C([H])=C([H])C([H])=C1[H] 0.000 claims description 11
- 125000005500 uronium group Chemical group 0.000 claims description 10
- 125000002777 acetyl group Chemical group [H]C([H])([H])C(*)=O 0.000 claims description 9
- 239000003054 catalyst Substances 0.000 claims description 9
- 125000005842 heteroatom Chemical group 0.000 claims description 9
- 238000004519 manufacturing process Methods 0.000 claims description 9
- 239000012038 nucleophile Substances 0.000 claims description 9
- 238000004064 recycling Methods 0.000 claims description 9
- 229920006395 saturated elastomer Polymers 0.000 claims description 9
- 239000011324 bead Substances 0.000 claims description 8
- 229910052799 carbon Inorganic materials 0.000 claims description 8
- ASOKPJOREAFHNY-UHFFFAOYSA-N 1-Hydroxybenzotriazole Chemical compound C1=CC=C2N(O)N=NC2=C1 ASOKPJOREAFHNY-UHFFFAOYSA-N 0.000 claims description 7
- NQTADLQHYWFPDB-UHFFFAOYSA-N N-Hydroxysuccinimide Chemical compound ON1C(=O)CCC1=O NQTADLQHYWFPDB-UHFFFAOYSA-N 0.000 claims description 7
- NPZTUJOABDZTLV-UHFFFAOYSA-N hydroxybenzotriazole Substances O=C1C=CC=C2NNN=C12 NPZTUJOABDZTLV-UHFFFAOYSA-N 0.000 claims description 7
- CWXZAJNUTOBAOI-UHFFFAOYSA-N 1-(2,3-dimethoxyphenyl)-2-hydroxy-2-phenylethanone Chemical compound COC1=CC=CC(C(=O)C(O)C=2C=CC=CC=2)=C1OC CWXZAJNUTOBAOI-UHFFFAOYSA-N 0.000 claims description 6
- YQTCQNIPQMJNTI-UHFFFAOYSA-N 2,2-dimethylpropan-1-one Chemical group CC(C)(C)[C]=O YQTCQNIPQMJNTI-UHFFFAOYSA-N 0.000 claims description 6
- 125000003903 2-propenyl group Chemical group [H]C([*])([H])C([H])=C([H])[H] 0.000 claims description 6
- XVWCUQLMLHHNEI-UHFFFAOYSA-N [1-(1,3-benzodioxol-5-yl)-1-nitroethyl] hydrogen carbonate Chemical compound OC(=O)OC(C)([N+]([O-])=O)C1=CC=C2OCOC2=C1 XVWCUQLMLHHNEI-UHFFFAOYSA-N 0.000 claims description 6
- 125000003236 benzoyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C(*)=O 0.000 claims description 6
- 125000001797 benzyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C([H])([H])* 0.000 claims description 6
- UWPVXVOVYSFGGG-UHFFFAOYSA-N carbonic acid;1-(2,3-dimethoxyphenyl)-2-hydroxy-2-phenylethanone Chemical compound OC(O)=O.COC1=CC=CC(C(=O)C(O)C=2C=CC=CC=2)=C1OC UWPVXVOVYSFGGG-UHFFFAOYSA-N 0.000 claims description 6
- 125000002668 chloroacetyl group Chemical group ClCC(=O)* 0.000 claims description 6
- 229920006037 cross link polymer Polymers 0.000 claims description 6
- 125000004184 methoxymethyl group Chemical group [H]C([H])([H])OC([H])([H])* 0.000 claims description 6
- 125000004092 methylthiomethyl group Chemical group [H]C([H])([H])SC([H])([H])* 0.000 claims description 6
- 239000000377 silicon dioxide Substances 0.000 claims description 6
- 125000001412 tetrahydropyranyl group Chemical group 0.000 claims description 6
- 125000004044 trifluoroacetyl group Chemical group FC(C(=O)*)(F)F 0.000 claims description 6
- 125000003088 (fluoren-9-ylmethoxy)carbonyl group Chemical group 0.000 claims description 5
- BDNKZNFMNDZQMI-UHFFFAOYSA-N 1,3-diisopropylcarbodiimide Chemical compound CC(C)N=C=NC(C)C BDNKZNFMNDZQMI-UHFFFAOYSA-N 0.000 claims description 5
- OKTJSMMVPCPJKN-UHFFFAOYSA-N Carbon Chemical compound [C] OKTJSMMVPCPJKN-UHFFFAOYSA-N 0.000 claims description 5
- QOSSAOTZNIDXMA-UHFFFAOYSA-N Dicylcohexylcarbodiimide Chemical compound C1CCCCC1N=C=NC1CCCCC1 QOSSAOTZNIDXMA-UHFFFAOYSA-N 0.000 claims description 5
- UFHFLCQGNIYNRP-UHFFFAOYSA-N Hydrogen Chemical compound [H][H] UFHFLCQGNIYNRP-UHFFFAOYSA-N 0.000 claims description 5
- 229910000323 aluminium silicate Inorganic materials 0.000 claims description 5
- BGRWYRAHAFMIBJ-UHFFFAOYSA-N diisopropylcarbodiimide Natural products CC(C)NC(=O)NC(C)C BGRWYRAHAFMIBJ-UHFFFAOYSA-N 0.000 claims description 5
- 239000011521 glass Substances 0.000 claims description 5
- 229910044991 metal oxide Inorganic materials 0.000 claims description 5
- 150000004706 metal oxides Chemical class 0.000 claims description 5
- 239000005373 porous glass Substances 0.000 claims description 5
- 125000000025 triisopropylsilyl group Chemical group C(C)(C)[Si](C(C)C)(C(C)C)* 0.000 claims description 5
- 239000007821 HATU Substances 0.000 claims description 4
- 125000004391 aryl sulfonyl group Chemical group 0.000 claims description 4
- 125000005524 levulinyl group Chemical group 0.000 claims description 4
- 150000003839 salts Chemical class 0.000 claims description 4
- 125000000026 trimethylsilyl group Chemical group [H]C([H])([H])[Si]([*])(C([H])([H])[H])C([H])([H])[H] 0.000 claims description 4
- 150000008065 acid anhydrides Chemical class 0.000 claims description 3
- 150000001718 carbodiimides Chemical class 0.000 claims description 3
- 125000006501 nitrophenyl group Chemical group 0.000 claims description 3
- 108020004707 nucleic acids Proteins 0.000 claims description 3
- 102000039446 nucleic acids Human genes 0.000 claims description 3
- 150000007523 nucleic acids Chemical class 0.000 claims description 3
- 125000000538 pentafluorophenyl group Chemical group FC1=C(F)C(F)=C(*)C(F)=C1F 0.000 claims description 3
- RGSFGYAAUTVSQA-UHFFFAOYSA-N pentamethylene Natural products C1CCCC1 RGSFGYAAUTVSQA-UHFFFAOYSA-N 0.000 claims description 3
- XYFCBTPGUUZFHI-UHFFFAOYSA-O phosphonium Chemical compound [PH4+] XYFCBTPGUUZFHI-UHFFFAOYSA-O 0.000 claims description 3
- LMBFAGIMSUYTBN-MPZNNTNKSA-N teixobactin Chemical compound C([C@H](C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CO)C(=O)N[C@H](CCC(N)=O)C(=O)N[C@H]([C@@H](C)CC)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CO)C(=O)N[C@H]1C(N[C@@H](C)C(=O)N[C@@H](C[C@@H]2NC(=N)NC2)C(=O)N[C@H](C(=O)O[C@H]1C)[C@@H](C)CC)=O)NC)C1=CC=CC=C1 LMBFAGIMSUYTBN-MPZNNTNKSA-N 0.000 claims description 3
- 150000003852 triazoles Chemical class 0.000 claims description 3
- HJBLUNHMOKFZQX-UHFFFAOYSA-N 3-hydroxy-1,2,3-benzotriazin-4-one Chemical compound C1=CC=C2C(=O)N(O)N=NC2=C1 HJBLUNHMOKFZQX-UHFFFAOYSA-N 0.000 claims description 2
- PVJZBZSCGJAWNG-UHFFFAOYSA-N 2,4,6-trimethylbenzenesulfonyl chloride Chemical compound CC1=CC(C)=C(S(Cl)(=O)=O)C(C)=C1 PVJZBZSCGJAWNG-UHFFFAOYSA-N 0.000 claims 6
- RAXXELZNTBOGNW-UHFFFAOYSA-N imidazole Natural products C1=CNC=N1 RAXXELZNTBOGNW-UHFFFAOYSA-N 0.000 claims 6
- CSKNSYBAZOQPLR-UHFFFAOYSA-N benzenesulfonyl chloride Chemical compound ClS(=O)(=O)C1=CC=CC=C1 CSKNSYBAZOQPLR-UHFFFAOYSA-N 0.000 claims 5
- IJOOHPMOJXWVHK-UHFFFAOYSA-N chlorotrimethylsilane Chemical compound C[Si](C)(C)Cl IJOOHPMOJXWVHK-UHFFFAOYSA-N 0.000 claims 4
- PSHKMPUSSFXUIA-UHFFFAOYSA-N n,n-dimethylpyridin-2-amine Chemical compound CN(C)C1=CC=CC=N1 PSHKMPUSSFXUIA-UHFFFAOYSA-N 0.000 claims 4
- NGNBDVOYPDDBFK-UHFFFAOYSA-N 2-[2,4-di(pentan-2-yl)phenoxy]acetyl chloride Chemical compound CCCC(C)C1=CC=C(OCC(Cl)=O)C(C(C)CCC)=C1 NGNBDVOYPDDBFK-UHFFFAOYSA-N 0.000 claims 2
- CFMZSMGAMPBRBE-UHFFFAOYSA-N 2-hydroxyisoindole-1,3-dione Chemical compound C1=CC=C2C(=O)N(O)C(=O)C2=C1 CFMZSMGAMPBRBE-UHFFFAOYSA-N 0.000 claims 2
- NYVWYZMUMRFMRR-UHFFFAOYSA-N 4-(iminomethylideneamino)-n,n-dimethylpentan-1-amine Chemical compound N=C=NC(C)CCCN(C)C NYVWYZMUMRFMRR-UHFFFAOYSA-N 0.000 claims 2
- YXFWFUSVDJIVIV-UHFFFAOYSA-N 4-nitro-2h-triazole Chemical compound [O-][N+](=O)C=1C=NNN=1 YXFWFUSVDJIVIV-UHFFFAOYSA-N 0.000 claims 2
- ANMJUTPNRJKVNS-UHFFFAOYSA-N [dimethylamino(hydroxy)methylidene]-dimethylazanium;chloride Chemical compound Cl.CN(C)C(=O)N(C)C ANMJUTPNRJKVNS-UHFFFAOYSA-N 0.000 claims 2
- 150000008064 anhydrides Chemical class 0.000 claims 2
- PPQNDCSTOHZQEH-UHFFFAOYSA-N bis(benzotriazol-1-yl) carbonate Chemical class N1=NC2=CC=CC=C2N1OC(=O)ON1C2=CC=CC=C2N=N1 PPQNDCSTOHZQEH-UHFFFAOYSA-N 0.000 claims 2
- 125000004360 trifluorophenyl group Chemical group 0.000 claims 2
- GKQLYSROISKDLL-UHFFFAOYSA-N EEDQ Chemical compound C1=CC=C2N(C(=O)OCC)C(OCC)C=CC2=C1 GKQLYSROISKDLL-UHFFFAOYSA-N 0.000 claims 1
- RYXPMWYHEBGTRV-UHFFFAOYSA-N Omeprazole sodium Chemical compound [Na+].N=1C2=CC(OC)=CC=C2[N-]C=1S(=O)CC1=NC=C(C)C(OC)=C1C RYXPMWYHEBGTRV-UHFFFAOYSA-N 0.000 claims 1
- 125000003835 nucleoside group Chemical group 0.000 abstract description 4
- 239000003153 chemical reaction reagent Substances 0.000 description 36
- OKKJLVBELUTLKV-UHFFFAOYSA-N Methanol Chemical compound OC OKKJLVBELUTLKV-UHFFFAOYSA-N 0.000 description 33
- WEVYAHXRMPXWCK-UHFFFAOYSA-N Acetonitrile Chemical compound CC#N WEVYAHXRMPXWCK-UHFFFAOYSA-N 0.000 description 29
- 230000015572 biosynthetic process Effects 0.000 description 22
- HEDRZPFGACZZDS-UHFFFAOYSA-N Chloroform Chemical compound ClC(Cl)Cl HEDRZPFGACZZDS-UHFFFAOYSA-N 0.000 description 20
- 239000000243 solution Substances 0.000 description 19
- 238000003786 synthesis reaction Methods 0.000 description 19
- JUJWROOIHBZHMG-UHFFFAOYSA-N Pyridine Chemical compound C1=CC=NC=C1 JUJWROOIHBZHMG-UHFFFAOYSA-N 0.000 description 17
- 238000006243 chemical reaction Methods 0.000 description 17
- OISVCGZHLKNMSJ-UHFFFAOYSA-N 2,6-dimethylpyridine Chemical compound CC1=CC=CC(C)=N1 OISVCGZHLKNMSJ-UHFFFAOYSA-N 0.000 description 15
- 238000003776 cleavage reaction Methods 0.000 description 13
- 230000007017 scission Effects 0.000 description 13
- VHUUQVKOLVNVRT-UHFFFAOYSA-N Ammonium hydroxide Chemical compound [NH4+].[OH-] VHUUQVKOLVNVRT-UHFFFAOYSA-N 0.000 description 12
- 239000000908 ammonium hydroxide Substances 0.000 description 12
- 238000011068 loading method Methods 0.000 description 11
- 230000008929 regeneration Effects 0.000 description 9
- 238000011069 regeneration method Methods 0.000 description 9
- ZMANZCXQSJIPKH-UHFFFAOYSA-N Triethylamine Chemical compound CCN(CC)CC ZMANZCXQSJIPKH-UHFFFAOYSA-N 0.000 description 8
- 239000005289 controlled pore glass Substances 0.000 description 8
- 239000000047 product Substances 0.000 description 8
- UMJSCPRVCHMLSP-UHFFFAOYSA-N pyridine Natural products COC1=CC=CN=C1 UMJSCPRVCHMLSP-UHFFFAOYSA-N 0.000 description 8
- 238000004458 analytical method Methods 0.000 description 7
- 230000007062 hydrolysis Effects 0.000 description 7
- 238000006460 hydrolysis reaction Methods 0.000 description 7
- WFDIJRYMOXRFFG-UHFFFAOYSA-N Acetic anhydride Chemical compound CC(=O)OC(C)=O WFDIJRYMOXRFFG-UHFFFAOYSA-N 0.000 description 6
- QGZKDVFQNNGYKY-UHFFFAOYSA-N Ammonia Chemical compound N QGZKDVFQNNGYKY-UHFFFAOYSA-N 0.000 description 6
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 description 6
- 239000002253 acid Substances 0.000 description 6
- BWHMMNNQKKPAPP-UHFFFAOYSA-L potassium carbonate Chemical compound [K+].[K+].[O-]C([O-])=O BWHMMNNQKKPAPP-UHFFFAOYSA-L 0.000 description 6
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 6
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 6
- XWKFPIODWVPXLX-UHFFFAOYSA-N 2-methyl-5-methylpyridine Natural products CC1=CC=C(C)N=C1 XWKFPIODWVPXLX-UHFFFAOYSA-N 0.000 description 5
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 5
- 239000000562 conjugate Substances 0.000 description 5
- 230000000694 effects Effects 0.000 description 5
- CTSLXHKWHWQRSH-UHFFFAOYSA-N oxalyl chloride Substances ClC(=O)C(Cl)=O CTSLXHKWHWQRSH-UHFFFAOYSA-N 0.000 description 5
- 230000003252 repetitive effect Effects 0.000 description 5
- HEMHJVSKTPXQMS-UHFFFAOYSA-M sodium hydroxide Inorganic materials [OH-].[Na+] HEMHJVSKTPXQMS-UHFFFAOYSA-M 0.000 description 5
- PNVPNXKRAUBJGW-UHFFFAOYSA-N (2-chloroacetyl) 2-chloroacetate Chemical compound ClCC(=O)OC(=O)CCl PNVPNXKRAUBJGW-UHFFFAOYSA-N 0.000 description 4
- PEHFQQWAINXOQG-UHFFFAOYSA-N (2-methoxyacetyl) 2-methoxyacetate Chemical compound COCC(=O)OC(=O)COC PEHFQQWAINXOQG-UHFFFAOYSA-N 0.000 description 4
- 150000001408 amides Chemical class 0.000 description 4
- 238000001212 derivatisation Methods 0.000 description 4
- JXTHNDFMNIQAHM-UHFFFAOYSA-N dichloroacetic acid Chemical compound OC(=O)C(Cl)Cl JXTHNDFMNIQAHM-UHFFFAOYSA-N 0.000 description 4
- 239000006260 foam Substances 0.000 description 4
- 239000000463 material Substances 0.000 description 4
- 238000010532 solid phase synthesis reaction Methods 0.000 description 4
- RYYWUUFWQRZTIU-UHFFFAOYSA-K thiophosphate Chemical compound [O-]P([O-])([O-])=S RYYWUUFWQRZTIU-UHFFFAOYSA-K 0.000 description 4
- DNXOCFKTVLHUMU-UHFFFAOYSA-N 2-[4-(carboxymethoxy)phenoxy]acetic acid Chemical compound OC(=O)COC1=CC=C(OCC(O)=O)C=C1 DNXOCFKTVLHUMU-UHFFFAOYSA-N 0.000 description 3
- PEDCQBHIVMGVHV-UHFFFAOYSA-N Glycerine Chemical compound OCC(O)CO PEDCQBHIVMGVHV-UHFFFAOYSA-N 0.000 description 3
- CSNNHWWHGAXBCP-UHFFFAOYSA-L Magnesium sulfate Chemical compound [Mg+2].[O-][S+2]([O-])([O-])[O-] CSNNHWWHGAXBCP-UHFFFAOYSA-L 0.000 description 3
- JGFZNNIVVJXRND-UHFFFAOYSA-N N,N-Diisopropylethylamine (DIPEA) Chemical compound CCN(C(C)C)C(C)C JGFZNNIVVJXRND-UHFFFAOYSA-N 0.000 description 3
- KWYUFKZDYYNOTN-UHFFFAOYSA-M Potassium hydroxide Chemical compound [OH-].[K+] KWYUFKZDYYNOTN-UHFFFAOYSA-M 0.000 description 3
- 229910021529 ammonia Inorganic materials 0.000 description 3
- 125000002843 carboxylic acid group Chemical group 0.000 description 3
- 239000003921 oil Substances 0.000 description 3
- 238000010647 peptide synthesis reaction Methods 0.000 description 3
- 229910000027 potassium carbonate Inorganic materials 0.000 description 3
- 108090000765 processed proteins & peptides Proteins 0.000 description 3
- 239000002904 solvent Substances 0.000 description 3
- 238000003756 stirring Methods 0.000 description 3
- NWUYHJFMYQTDRP-UHFFFAOYSA-N 1,2-bis(ethenyl)benzene;1-ethenyl-2-ethylbenzene;styrene Chemical compound C=CC1=CC=CC=C1.CCC1=CC=CC=C1C=C.C=CC1=CC=CC=C1C=C NWUYHJFMYQTDRP-UHFFFAOYSA-N 0.000 description 2
- LOSXTWDYAWERDB-UHFFFAOYSA-N 1-[chloro(diphenyl)methyl]-2,3-dimethoxybenzene Chemical compound COC1=CC=CC(C(Cl)(C=2C=CC=CC=2)C=2C=CC=CC=2)=C1OC LOSXTWDYAWERDB-UHFFFAOYSA-N 0.000 description 2
- ZDHCZVWCTKTBRY-UHFFFAOYSA-N 12-hydroxylauric acid Chemical compound OCCCCCCCCCCCC(O)=O ZDHCZVWCTKTBRY-UHFFFAOYSA-N 0.000 description 2
- ROSDSFDQCJNGOL-UHFFFAOYSA-N Dimethylamine Chemical compound CNC ROSDSFDQCJNGOL-UHFFFAOYSA-N 0.000 description 2
- UQSXHKLRYXJYBZ-UHFFFAOYSA-N Iron oxide Chemical compound [Fe]=O UQSXHKLRYXJYBZ-UHFFFAOYSA-N 0.000 description 2
- BAVYZALUXZFZLV-UHFFFAOYSA-N Methylamine Chemical compound NC BAVYZALUXZFZLV-UHFFFAOYSA-N 0.000 description 2
- MUBZPKHOEPUJKR-UHFFFAOYSA-N Oxalic acid Chemical compound OC(=O)C(O)=O MUBZPKHOEPUJKR-UHFFFAOYSA-N 0.000 description 2
- 239000004793 Polystyrene Substances 0.000 description 2
- UIIMBOGNXHQVGW-UHFFFAOYSA-M Sodium bicarbonate Chemical compound [Na+].OC([O-])=O UIIMBOGNXHQVGW-UHFFFAOYSA-M 0.000 description 2
- 238000002835 absorbance Methods 0.000 description 2
- 230000004913 activation Effects 0.000 description 2
- 238000013459 approach Methods 0.000 description 2
- 125000003178 carboxy group Chemical group [H]OC(*)=O 0.000 description 2
- 150000001732 carboxylic acid derivatives Chemical class 0.000 description 2
- 230000008878 coupling Effects 0.000 description 2
- 238000010168 coupling process Methods 0.000 description 2
- 238000005859 coupling reaction Methods 0.000 description 2
- 238000006642 detritylation reaction Methods 0.000 description 2
- 229960005215 dichloroacetic acid Drugs 0.000 description 2
- 150000002118 epoxides Chemical class 0.000 description 2
- 238000010353 genetic engineering Methods 0.000 description 2
- 230000006872 improvement Effects 0.000 description 2
- 230000000977 initiatory effect Effects 0.000 description 2
- VLKZOEOYAKHREP-UHFFFAOYSA-N n-Hexane Chemical class CCCCCC VLKZOEOYAKHREP-UHFFFAOYSA-N 0.000 description 2
- 229910052760 oxygen Inorganic materials 0.000 description 2
- 230000037361 pathway Effects 0.000 description 2
- VLTRZXGMWDSKGL-UHFFFAOYSA-N perchloric acid Chemical compound OCl(=O)(=O)=O VLTRZXGMWDSKGL-UHFFFAOYSA-N 0.000 description 2
- 239000012071 phase Substances 0.000 description 2
- 229920002223 polystyrene Polymers 0.000 description 2
- 102000004196 processed proteins & peptides Human genes 0.000 description 2
- 238000012552 review Methods 0.000 description 2
- 239000002002 slurry Substances 0.000 description 2
- 159000000000 sodium salts Chemical class 0.000 description 2
- 230000002269 spontaneous effect Effects 0.000 description 2
- KDYFGRWQOYBRFD-UHFFFAOYSA-N succinic acid Chemical compound OC(=O)CCC(O)=O KDYFGRWQOYBRFD-UHFFFAOYSA-N 0.000 description 2
- FPGGTKZVZWFYPV-UHFFFAOYSA-M tetrabutylammonium fluoride Chemical compound [F-].CCCC[N+](CCCC)(CCCC)CCCC FPGGTKZVZWFYPV-UHFFFAOYSA-M 0.000 description 2
- GETQZCLCWQTVFV-UHFFFAOYSA-N trimethylamine Chemical compound CN(C)C GETQZCLCWQTVFV-UHFFFAOYSA-N 0.000 description 2
- AVQQQNCBBIEMEU-UHFFFAOYSA-N 1,1,3,3-tetramethylurea Chemical compound CN(C)C(=O)N(C)C AVQQQNCBBIEMEU-UHFFFAOYSA-N 0.000 description 1
- JUDOLRSMWHVKGX-UHFFFAOYSA-N 1,1-dioxo-1$l^{6},2-benzodithiol-3-one Chemical compound C1=CC=C2C(=O)SS(=O)(=O)C2=C1 JUDOLRSMWHVKGX-UHFFFAOYSA-N 0.000 description 1
- WSLDOOZREJYCGB-UHFFFAOYSA-N 1,2-Dichloroethane Chemical compound ClCCCl WSLDOOZREJYCGB-UHFFFAOYSA-N 0.000 description 1
- PIYNUZCGMLCXKJ-UHFFFAOYSA-N 1,4-dioxane-2,6-dione Chemical compound O=C1COCC(=O)O1 PIYNUZCGMLCXKJ-UHFFFAOYSA-N 0.000 description 1
- FPIRBHDGWMWJEP-UHFFFAOYSA-N 1-hydroxy-7-azabenzotriazole Chemical compound C1=CN=C2N(O)N=NC2=C1 FPIRBHDGWMWJEP-UHFFFAOYSA-N 0.000 description 1
- FALRKNHUBBKYCC-UHFFFAOYSA-N 2-(chloromethyl)pyridine-3-carbonitrile Chemical compound ClCC1=NC=CC=C1C#N FALRKNHUBBKYCC-UHFFFAOYSA-N 0.000 description 1
- SHKUUQIDMUMQQK-UHFFFAOYSA-N 2-[4-(oxiran-2-ylmethoxy)butoxymethyl]oxirane Chemical compound C1OC1COCCCCOCC1CO1 SHKUUQIDMUMQQK-UHFFFAOYSA-N 0.000 description 1
- 125000004080 3-carboxypropanoyl group Chemical group O=C([*])C([H])([H])C([H])([H])C(O[H])=O 0.000 description 1
- BTJIUGUIPKRLHP-UHFFFAOYSA-N 4-nitrophenol Chemical compound OC1=CC=C([N+]([O-])=O)C=C1 BTJIUGUIPKRLHP-UHFFFAOYSA-N 0.000 description 1
- HMFHBZSHGGEWLO-SOOFDHNKSA-N D-ribofuranose Chemical compound OC[C@H]1OC(O)[C@H](O)[C@@H]1O HMFHBZSHGGEWLO-SOOFDHNKSA-N 0.000 description 1
- 230000006820 DNA synthesis Effects 0.000 description 1
- QEVGZEDELICMKH-UHFFFAOYSA-N Diglycolic acid Chemical compound OC(=O)COCC(O)=O QEVGZEDELICMKH-UHFFFAOYSA-N 0.000 description 1
- IMROMDMJAWUWLK-UHFFFAOYSA-N Ethenol Chemical compound OC=C IMROMDMJAWUWLK-UHFFFAOYSA-N 0.000 description 1
- PIICEJLVQHRZGT-UHFFFAOYSA-N Ethylenediamine Chemical compound NCCN PIICEJLVQHRZGT-UHFFFAOYSA-N 0.000 description 1
- KRHYYFGTRYWZRS-UHFFFAOYSA-M Fluoride anion Chemical compound [F-] KRHYYFGTRYWZRS-UHFFFAOYSA-M 0.000 description 1
- DGAQECJNVWCQMB-PUAWFVPOSA-M Ilexoside XXIX Chemical compound C[C@@H]1CC[C@@]2(CC[C@@]3(C(=CC[C@H]4[C@]3(CC[C@@H]5[C@@]4(CC[C@@H](C5(C)C)OS(=O)(=O)[O-])C)C)[C@@H]2[C@]1(C)O)C)C(=O)O[C@H]6[C@@H]([C@H]([C@@H]([C@H](O6)CO)O)O)O.[Na+] DGAQECJNVWCQMB-PUAWFVPOSA-M 0.000 description 1
- ZRMYHUFDVLRYPN-UHFFFAOYSA-N O=C(C1C2C1)OC2=O Chemical compound O=C(C1C2C1)OC2=O ZRMYHUFDVLRYPN-UHFFFAOYSA-N 0.000 description 1
- 239000004952 Polyamide Substances 0.000 description 1
- 239000004721 Polyphenylene oxide Substances 0.000 description 1
- PYMYPHUHKUWMLA-LMVFSUKVSA-N Ribose Natural products OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PYMYPHUHKUWMLA-LMVFSUKVSA-N 0.000 description 1
- XUIMIQQOPSSXEZ-UHFFFAOYSA-N Silicon Chemical compound [Si] XUIMIQQOPSSXEZ-UHFFFAOYSA-N 0.000 description 1
- 239000012317 TBTU Substances 0.000 description 1
- CLZISMQKJZCZDN-UHFFFAOYSA-N [benzotriazol-1-yloxy(dimethylamino)methylidene]-dimethylazanium Chemical compound C1=CC=C2N(OC(N(C)C)=[N+](C)C)N=NC2=C1 CLZISMQKJZCZDN-UHFFFAOYSA-N 0.000 description 1
- 239000000654 additive Substances 0.000 description 1
- 230000000996 additive effect Effects 0.000 description 1
- 150000003973 alkyl amines Chemical class 0.000 description 1
- HMFHBZSHGGEWLO-UHFFFAOYSA-N alpha-D-Furanose-Ribose Natural products OCC1OC(O)C(O)C1O HMFHBZSHGGEWLO-UHFFFAOYSA-N 0.000 description 1
- 150000001413 amino acids Chemical class 0.000 description 1
- 125000003277 amino group Chemical group 0.000 description 1
- 239000008346 aqueous phase Substances 0.000 description 1
- 230000008901 benefit Effects 0.000 description 1
- WPYMKLBDIGXBTP-UHFFFAOYSA-N benzoic acid group Chemical group C(C1=CC=CC=C1)(=O)O WPYMKLBDIGXBTP-UHFFFAOYSA-N 0.000 description 1
- 230000000903 blocking effect Effects 0.000 description 1
- 239000001273 butane Substances 0.000 description 1
- WERYXYBDKMZEQL-UHFFFAOYSA-N butane-1,4-diol Chemical compound OCCCCO WERYXYBDKMZEQL-UHFFFAOYSA-N 0.000 description 1
- 150000001733 carboxylic acid esters Chemical class 0.000 description 1
- 150000001735 carboxylic acids Chemical class 0.000 description 1
- 239000003729 cation exchange resin Substances 0.000 description 1
- 238000005119 centrifugation Methods 0.000 description 1
- FOCAUTSVDIKZOP-UHFFFAOYSA-N chloroacetic acid Chemical compound OC(=O)CCl FOCAUTSVDIKZOP-UHFFFAOYSA-N 0.000 description 1
- 239000004927 clay Substances 0.000 description 1
- 239000013058 crude material Substances 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 230000007547 defect Effects 0.000 description 1
- 239000005549 deoxyribonucleoside Substances 0.000 description 1
- 150000005690 diesters Chemical class 0.000 description 1
- NAGJZTKCGNOGPW-UHFFFAOYSA-K dioxido-sulfanylidene-sulfido-$l^{5}-phosphane Chemical compound [O-]P([O-])([S-])=S NAGJZTKCGNOGPW-UHFFFAOYSA-K 0.000 description 1
- 230000008034 disappearance Effects 0.000 description 1
- 238000001035 drying Methods 0.000 description 1
- 238000001962 electrophoresis Methods 0.000 description 1
- 238000010828 elution Methods 0.000 description 1
- 239000000839 emulsion Substances 0.000 description 1
- RTZKZFJDLAIYFH-UHFFFAOYSA-N ether Substances CCOCC RTZKZFJDLAIYFH-UHFFFAOYSA-N 0.000 description 1
- 238000001704 evaporation Methods 0.000 description 1
- 230000008020 evaporation Effects 0.000 description 1
- 238000002474 experimental method Methods 0.000 description 1
- 238000001914 filtration Methods 0.000 description 1
- 238000001502 gel electrophoresis Methods 0.000 description 1
- IKGLACJFEHSFNN-UHFFFAOYSA-N hydron;triethylazanium;trifluoride Chemical compound F.F.F.CCN(CC)CC IKGLACJFEHSFNN-UHFFFAOYSA-N 0.000 description 1
- 239000012535 impurity Substances 0.000 description 1
- 229910003480 inorganic solid Inorganic materials 0.000 description 1
- 239000003456 ion exchange resin Substances 0.000 description 1
- 229920003303 ion-exchange polymer Polymers 0.000 description 1
- 239000007791 liquid phase Substances 0.000 description 1
- 229910052943 magnesium sulfate Inorganic materials 0.000 description 1
- 235000019341 magnesium sulphate Nutrition 0.000 description 1
- 229920003145 methacrylic acid copolymer Polymers 0.000 description 1
- 229940117841 methacrylic acid copolymer Drugs 0.000 description 1
- POULHZVOKOAJMA-UHFFFAOYSA-N methyl undecanoic acid Natural products CCCCCCCCCCCC(O)=O POULHZVOKOAJMA-UHFFFAOYSA-N 0.000 description 1
- IJDNQMDRQITEOD-UHFFFAOYSA-N n-butane Chemical compound CCCC IJDNQMDRQITEOD-UHFFFAOYSA-N 0.000 description 1
- OFBQJSOFQDEBGM-UHFFFAOYSA-N n-pentane Natural products CCCCC OFBQJSOFQDEBGM-UHFFFAOYSA-N 0.000 description 1
- 230000007935 neutral effect Effects 0.000 description 1
- 229910000480 nickel oxide Inorganic materials 0.000 description 1
- 239000012011 nucleophilic catalyst Substances 0.000 description 1
- 235000006408 oxalic acid Nutrition 0.000 description 1
- 125000003431 oxalo group Chemical group 0.000 description 1
- TWNQGVIAIRXVLR-UHFFFAOYSA-N oxo(oxoalumanyloxy)alumane Chemical compound O=[Al]O[Al]=O TWNQGVIAIRXVLR-UHFFFAOYSA-N 0.000 description 1
- GNRSAWUEBMWBQH-UHFFFAOYSA-N oxonickel Chemical compound [Ni]=O GNRSAWUEBMWBQH-UHFFFAOYSA-N 0.000 description 1
- 239000002245 particle Substances 0.000 description 1
- 239000000863 peptide conjugate Substances 0.000 description 1
- 150000002989 phenols Chemical class 0.000 description 1
- 125000003170 phenylsulfonyl group Chemical group C1(=CC=CC=C1)S(=O)(=O)* 0.000 description 1
- 150000008300 phosphoramidites Chemical class 0.000 description 1
- 239000002985 plastic film Substances 0.000 description 1
- 229920002647 polyamide Polymers 0.000 description 1
- 229920000570 polyether Polymers 0.000 description 1
- 229920001184 polypeptide Polymers 0.000 description 1
- 229920002451 polyvinyl alcohol Polymers 0.000 description 1
- 239000002244 precipitate Substances 0.000 description 1
- 238000001556 precipitation Methods 0.000 description 1
- 230000037452 priming Effects 0.000 description 1
- 102000004169 proteins and genes Human genes 0.000 description 1
- 108090000623 proteins and genes Proteins 0.000 description 1
- 238000000746 purification Methods 0.000 description 1
- 230000002441 reversible effect Effects 0.000 description 1
- 229910000077 silane Inorganic materials 0.000 description 1
- 239000000741 silica gel Substances 0.000 description 1
- 229910002027 silica gel Inorganic materials 0.000 description 1
- 229910052710 silicon Inorganic materials 0.000 description 1
- 239000010703 silicon Substances 0.000 description 1
- 229910000030 sodium bicarbonate Inorganic materials 0.000 description 1
- 235000017557 sodium bicarbonate Nutrition 0.000 description 1
- 239000012279 sodium borohydride Substances 0.000 description 1
- 229910000033 sodium borohydride Inorganic materials 0.000 description 1
- 239000007790 solid phase Substances 0.000 description 1
- 239000001384 succinic acid Substances 0.000 description 1
- 229940014800 succinic anhydride Drugs 0.000 description 1
- 229910052717 sulfur Inorganic materials 0.000 description 1
- RAHZWNYVWXNFOC-UHFFFAOYSA-N sulfur dioxide Inorganic materials O=S=O RAHZWNYVWXNFOC-UHFFFAOYSA-N 0.000 description 1
- ILMRJRBKQSSXGY-UHFFFAOYSA-N tert-butyl(dimethyl)silicon Chemical group C[Si](C)C(C)(C)C ILMRJRBKQSSXGY-UHFFFAOYSA-N 0.000 description 1
- YBRBMKDOPFTVDT-UHFFFAOYSA-N tert-butylamine Chemical compound CC(C)(C)N YBRBMKDOPFTVDT-UHFFFAOYSA-N 0.000 description 1
- 150000003512 tertiary amines Chemical class 0.000 description 1
- KBLZDCFTQSIIOH-UHFFFAOYSA-M tetrabutylazanium;perchlorate Chemical compound [O-]Cl(=O)(=O)=O.CCCC[N+](CCCC)(CCCC)CCCC KBLZDCFTQSIIOH-UHFFFAOYSA-M 0.000 description 1
- 150000003536 tetrazoles Chemical class 0.000 description 1
- UVZICZIVKIMRNE-UHFFFAOYSA-N thiodiacetic acid Chemical compound OC(=O)CSCC(O)=O UVZICZIVKIMRNE-UHFFFAOYSA-N 0.000 description 1
- 231100000331 toxic Toxicity 0.000 description 1
- 230000002588 toxic effect Effects 0.000 description 1
- 238000012546 transfer Methods 0.000 description 1
- 125000004665 trialkylsilyl group Chemical group 0.000 description 1
- 235000012431 wafers Nutrition 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
Definitions
- the present invention relates to a reusable solid support for oligonucleotide synthesis. In another of its aspects, the present invention relates to a process for production of such a reusable solid support. In yet another of its aspects, the present invention relates to a process for use of such a reusable solid support.
- succinyl linker arm has the following general formula:
- the succmyl group links the growing oligonucleotide from its terminal 3' hydroxyl group by an ester bond to a p ⁇ mary amme on the support, which may be, for example, conventional controlled pore glass (CPG) or silica, by an amide bond.
- CPG controlled pore glass
- the desired oligonucleotide is freed or cleaved from the succinyl linker arm hydrolyzmg the ester carbonyl group.
- the hydrolysis agent is usually concentrated ammonium hydroxide Typically, this reaction can take from 1 -4 hours to complete. With improvements to current solid-phase oligonucleotide synthesizers, this cleavage step can represent 50% or more of the total time require to synthesize the desired oligonucleotide.
- linker arm Another type of linker arm is disclosed in United States patent 5,112,962 [Letsmger et al. (Letsmger)], the contents of which are hereby incorporated by reference Letsmger teaches a linker arm for solid support synthesis of oligonucleotides and oligonucleotide de ⁇ vatives have the following formula
- oxalyl linker arm which purportedly release the synthesized oligonucleotide or oligonucleotide de ⁇ vate in a pe ⁇ od of 1-30 minutes in a manner that leaves the oligonucleotide fully protected
- the oxalyl linker arm purportedly can be rapidly cleaved by 5% ammonium hydroxide m methanol, ammonium hydroxide, wet tertiary amine, t ⁇ ethylamine/alcohol, t ⁇ ethylamme/methanol, t ⁇ ethylamine/ethanol, aqueous t ⁇ methylamme and other bases
- the oxalyl linker arm of Letsmger suffers fiom its purported advantage
- the present inventors have discovered that the oxalvl linker arm of Letsmger is susceptible to significant spontaneous hydrolysis (e g spontaneous hydrolysis of ⁇ 10-40° o per month) which
- linker arm is not reusable after production and cleavage of the desired oligonucleotide
- conventional linker arms may be regarded as non- recyclable
- Figure 1 illustrates the conventional use of a succinyl linker arm for the production of an oligonucleotide
- the support is irreversibly linked to the linker compound (I e . the succinyl moiety) and cannot be reused
- linker arm for solid support oligonucleotide synthesis, which linker arm is recyclable. More specifically, the art is in need of a linker arm capable of repeated oligonucleotide synthesis/cleavage.
- R 8 is selected from the group consisting of a substituted or unsubstituted C,-C 20 alkyl group, a substituted or unsubstituted C 5 - C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group
- X 3 and X 4 are the same or different and are selected from the group consisting of -0-, -S-, -S(O) 2 - and -N(R 12 )-
- R 12 is selected from the group consisting of a substituted or unsubstituted C,-C 20 alkyl group, a substituted or unsubstituted C 5 -C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group
- Y is selected from the group consisting of:
- each step of the de ⁇ vatization described m the previous paragraph has the potential of incompletely de ⁇ vatizing each HX 4 - moiety on the support thereby increasing the likelihood of a heterogeneous surface Practically, it becomes necessary to block or cap unde ⁇ vatized HX 4 - moieties so that the linker moiety does interact with them Thus, the disadvantage is additional labour and cost required to effect de ⁇ vatization of the solid support
- a linker arm based on the de ⁇ vatized support desc ⁇ bed by Pon et al is not as resistant to partial cleavage du ⁇ ng regeneration as a de ⁇ vatized suppo ⁇ having a more fully saturated moiety
- It is an object of the present invention provide a novel linker arm for solid support oligonucleotide synthesis which obviates or mitigates at least one of the above-mentioned disadvantages of the prior art.
- the present invention provides a reusable linker arm for solid support oligonucleotide synthesis, the linker arm comprising the following formula:
- Z is a linker moiety and T is an organic radical.
- the present invention provides a reusable linker arm for solid support oligonucleotide synthesis, the linker arm comprising the following formula:
- the present invention provides a process for production of a reusable linker arm for oligonucleotide synthesis having the following formula:
- the present invention provides a process for production of a reusable linker arm for oligonucleotide synthesis having the following formula:
- the present invention provides a process for producing an oligonucleotide having a desired sequence comprising the steps of: (i) reacting a linker arm having the formula:
- Z is a linker moiety and T is an organic radical, with at least one oligonucleoside base until an oligonucleotide having the desired sequence is produce;
- oligonucleotide is intended to have a broad meaning and encompasses conventional oligonucleotides, backbone-modified oligonucleotides (e.g. phosphorothioate, phosphorodithioate and methyl-phophonate analogs useful as oligotherapeutic agents) and oligonucleotide derivatives such as oligonucleotide-peptide conjugates.
- backbone-modified oligonucleotides e.g. phosphorothioate, phosphorodithioate and methyl-phophonate analogs useful as oligotherapeutic agents
- oligonucleotide derivatives such as oligonucleotide-peptide conjugates.
- Figure 1 illustrates a specific process pathway for conventional oligonucleotide synthesis
- Figures 2 and 3 illustrate specific preferred embodiments of the present invention. BEST MODE FOR CARRYING OUT THE INVENTION
- Figure 1 illustrates a conventional process for solid support oligonucleotide synthesis
- a linking compound such as succmic acid (while succmic acid is illustrated, succmic anhyd ⁇ de may also be used)
- succmic anhyd ⁇ de may also be used
- the reaction results in the formation of an amide linkage between the linking compound and the support to produce succmyl-support conjugate
- the succmyl-support conjugate is reacted with a desired initial nucleoside to produce a linker arm
- DMT is dimethyoxyt ⁇ tyl
- B is the nucleobase
- R' is H (for deoxy ⁇ bonucleosides) or OR (for ⁇ bonucleosides) wherein R is H or a conventional blocking/ protecting group
- the reaction results in the formation of an ester linkage between the linking compound and the desired initial nucleoside at the 3' position of the latter
- the linker arm is then used m conventional oligonucleotide synthesis (e g in a conventional automated synthesizer) to produce an oligonucleotide of desired sequence attached to the linker arm
- the oligonucleotide is then cleaved from the linker by hydrolysis This serves to cleave the ester bond thereby freeing the oligonucleotide and an amine- termmated, non-reusable linker arm
- a support having a hydroxy-termmated functionality may be combined with a conventional linking compound to produce linker arm which may used to synthesize an oligonucleotide of desired sequence
- linker arm may be regenerated or recycled after cleavage of the oligonucleotide of desired sequence
- the reusable linker arm of the present invention has the following formula- Z— 0— T [SUPPORT]
- Z is a linker moiety and T is an organic radical.
- T contains at least one carbon.
- T is a C,-C 300 organic moiety, more preferably a C,-C 200 organic moiety, most preferably a C C ⁇ organic moiety.
- T may be a saturated or unsaturated organic moiety.
- T may contain one or more heteroatoms.
- T may comprise at least one heteroatom selected from N and O.
- the organic moiety in T comprises at least one moiety having the formula:
- the organic moiety in T comprises at least one moiety having the formula:
- the organic moiety in T comprises at least one moiety having the formula: ⁇ i l ⁇
- the organic moiety m T comp ⁇ ses at least one moiety having the formula
- the organic moiety in T comp ⁇ ses at least one moiety having the formula
- T may be unsubstituted or substituted
- the organic moiety of T may be substituted by at least one moiety selected from the group comp ⁇ smg a C ] -C 40 alkyl group, a C 5 -C 40 aryl group, a C,-C 40 alkoxy group, a C,-C 40 ester group, a C,-C 40 hydroxy group, a C 2 -C 40 acrylate group and a C,-C 40 alkylaryl group
- T has the formula
- T has the formula:
- a is 0 or 1
- Q is an organic moiety
- R 8 is hydrogen or a protecting group
- b is an integer having a value of 0-40.
- a may be 0 and R 8 may be hydrogen.
- a may be 1 and R 8 may be a protecting group.
- Non-limiting examples of protecting groups may be selected from the group comprising acetyl, chloroacetyl, methoxyacetyl, t-butyl phenoxyacetyl, phenoxyacetyl, trityl, methoxytrityl, dimethoxytrityl (DMT), dialkylphosphite, pivalyl-isobutyloxycarbonyl, f-butyldimethylsilyl, phenoxyacetal, 9- phenylxanthen-9-yl (pixyl), tetrahydropyranyl, methoxytetrahydropyranyl, methoxymethyl, benzyloxymethyl, methoxyethoxymethyl, methylthiomethyl, dialkylphosphate, levulinyl, dimethylphenylsilyl, trimethylsilyl, isopropyl- dimethylsilyl, diisopropylmethylsilyl, diethylisopropyls
- Q may be a moiety having the formula: - io-
- q, r, s, t and u are the same or different and each is an integer having a value of 0-40 and R a is selected from the group comprising hydrogen, hydroxyl, a C,-C 40 alkyl group, a C 5 -C 40 aryl group, a C 1 -C 40 alkoxy group, a C,-C 40 ester group, a C,-C 40 hydroxy group, a C 2 -C 40 acrylate group and a C 5 -C 40 alkylaryl group.
- s is 0, q, r and u are the same or different and each is an integer having a value of 1-10, t is an integer of 1-5 and R is hydroxyl.
- T has the formula:
- R 8 is selected from the group comprising hydrogen, hydroxyl, a C,-C 40 alkyl group, a C 5 -C 40 aryl group, a C,-
- C 40 alkoxy group a C [ -C 40 ester group,a C,-C 40 hydroxy group, a C 2 -C 40 acrylate group and a C 5 -C 40 alkylaryl group
- b is an integer having a value of 0-40.
- Q is a C,-C 100 organic moiety.
- Q may be a saturated organic moiety or an unsaturated organic moiety. It is preferreed that Q is a C,-C 100 organic moiety comprising at least one heteroatom selected from N and O.
- the organic moiety Q comprises at least one moiety having the formula: O
- the organic moiety Q comprises at least one moiety having the formula:
- organic moiety Q comp ⁇ ses at least one moiety having the formula:
- organic moiety Q comp ⁇ ses at least one moiety having the formula:
- organic moiety comp ⁇ ses at least one moiety having the formula:
- the organic moiety Q may unsubstituted or substituted.
- the organic moiety Q may be substituted by at least one moiety selected from the group comprising a C,-C 40 alkyl group, a C 5 -C 40 aryl group, a C,-C 40 alkoxy group, a C ⁇ -C 40 ester group, a C,- C 40 hydroxy group, a C 2 -C 40 acrylate group and a C 5 -C 40 alkylaryl group.
- Q has the formula:
- each of x, y and z is an integer having a value of 1-40.
- Z is a linker moiety.
- Z is derived from a linker compound have the general formula HO-Z-OH (Formula I below).
- the nature of the linker compound is not particularly restricted.
- linker moiety Z has the formula:
- this linker moiety may be derived from succinic acid or succinic anhydride.
- linker moiety Z has the following formula:
- this linker moiety may be derived from diglycolic acid or diglycolic anhydride.
- linker moiety Z has the following formula:
- this linker moiety may be derived from oxalic acid or oxalyl chloride.
- linker moiety Z has the following formula:
- R 1 , R 2 and R 3 are the same or different and are selected from the group consisting of hydrogen, halide, a substituted or unsubstituted C,-C 20 alkyl group, a substituted or unsubstituted C 5 -C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group;
- R 4 and R 5 are the same or different and are selected from the group consisting of hydrogen, a substituted or unsubstituted C,-C 20 alkyl group, a substituted or unsubstituted C 5 -C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group;
- X 1 is selected from the group consisting of -O-, -C(O)-, -S-, -S(O) 2 - and -N(R)-;
- R is selected hydrogen, a substituted or unsubstituted C,-
- X 2 is selected from the group consisting of -O-, -S-, -C(O)-, -S(O) 2 - and -N(R)-
- R is selected from the group comprising hydrogen, a substituted or unsubstituted C,-C 20 alkyl group, a substituted or unsubstituted C 5 - C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group
- R 6 and R 7 are the same or different and are selected from the group consisting of hydrogen, a substituted or unsubstituted C ⁇ -C 20 alkyl group, a substituted or unsubstituted C 5 -C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group
- m is 0, 1 or 2.
- B 1 preferably is selected from the group consisting of hydrogen, halide, a substituted or unsubstituted C,-C 20 alkyl group, a substituted or unsubstituted C 5 -C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group.
- at least one, more preferably each, of R, R 4 , R ⁇ R 6 and R 7 is hydrogen and preferably at least, more preferably both, of m and n are 1.
- each of R 1 , R 2 and R 3 is hydrogen and that X 1 and X 2 are both -O-.
- the most prefe ⁇ ed form of linker moiety Z is derived from hydroquinone-O,O'-diacetic acid.
- linker moiety Z has the following formula:
- R ⁇ R b and R' are the same or different and are selected from the group consisting of hydrogen, a substituted or unsubstituted C,-C 20 alkyl group, a substituted or unsubstituted C 5 -C 30 aryl group and a substituted or unsubstituted C 5 -C 40 alkylaryl group
- Y is selected from the group consisting of O, S, SO 2 and O-((CH 2 ),-O) q , 1 is an integer less than or equal to 60, q is an integer in the range of 1 - 1000, n and m are the same or different and are 1 or 2, with the proviso that, when Y is O, at least one of n and m is 2.
- 1 is an integer in the range of 1 - 10
- q is an integer in the range of 1 - 1000.
- the SUPPORT in the above formula is a conventional solid support.
- the nature of the solid support is not particularly restricted and is within the purview of a person skilled in the art.
- the solid support may be an inorganic substance.
- suitable inorganic substances may be selected from the group consisting of silica, porous glass, aluminosilicates, borosilicates, metal oxides (e.g. aluminum oxide, iron oxide, nickel oxide) and clay containing one or more of these.
- the solid support may be an organic substance such as a cross-linked polymer.
- Non-limiting examples of a suitable cross-linked polymer may be selected from the group consisting of polyamide, polyether, polystyrene and mixtures thereof
- the prefe ⁇ ed solid support for use herein is conventional and may be selected from controlled pore glass bead or polystyrene beads. Further, the support may be either in particle form (e.g., beads), three-dimensional slabs (e.g., polymeric inserts and foams) or in a flat two-dimensional like format (e.g., plastic sheets, glass chips, silicon wafers, etc.).
- the material used for the support may also be soluble in certain solvents (e.g., liquid-phase supports), but can be precipitated or crystallized from other solvents.
- linker arm (again, Z is a linker moiety and T is an organic radical), may then be reacted with a conventional nucleoside-linker compound to produce another linker arm according to the present invention.
- This other linker arm has the following formula:
- NUCLEOSIDE is a moiety selected from one of the following formulae:
- R 6 and R 10 are the same or different and are hydrogen or a protecting group
- R is hydrogen (for deoxy ⁇ bonucleosides or DNA) or -OR 11 (for ⁇ bonucleosides or RNA) wherein R 11 is hydrogen or a protecting group
- the linker can be attached to either the 5'-, 3'- or (if ribose) 2'- hvdroxyl positions Indeed, for RNA sequences, it makes little difference whether the ester linker formed between the nucleoside and the linker compound is at the 2'- or 3'- hydroxyl position of the nucleoside
- the nucleoside may be protected or blocked at the va ⁇ ous of its hydroxyl moieties
- Non- mitmg examples of useful protecting groups may be selected from the group consisting of acetyl, chloioacetyl, methoxyacetyl, t-butyl phenoxyacetyl, phenoxyacetyl, t ⁇ tyl, methoxyt ⁇ tyl, dimethoxyt ⁇ tyl (DMT), dialkylphosphite, pivalyl-isobutyloxvcarbonyl, r-butyldimethvlsilyl, phenoxyacetal, 9-phenylxanthen-9-yl (pixyl), tetrahydropyranyl, methoxvtetrahydropyranyl, methoxymethyl, benzyloxymethyl, methoxyethoxymethyl, methylthiomethyl, dialkylphosphate, levulmyl, dimethylphenylsilyl, t ⁇ methylsilyl, isopropyldimethylsilyl, diisopropyl
- the prefe ⁇ ed protecting group for desired 5'-hydroxyl position(s) is the acid labile dimethoxytrityl group.
- the prefe ⁇ ed protecting groups for these positions are trialkylsilyl (i.e. t-butyldimethylsilyl) or acetyl. Additional information may be obtained from the following references:
- a prefe ⁇ ed method for production of deoxy ⁇ bonucleosides in the context of the present invention is to use a nucleoside with a 5'-d ⁇ methoxytntyl protecting group and an appropnate exocychc amino protecting group, e g , N 6 -benzoyl-5'- d ⁇ methoxyt ⁇ tyl-2'-deoxyadenos ⁇ ne, N 4 -benzoyl-5'-d ⁇ methoxyt ⁇ tyl-2'- deoxycytidme, 5'-d ⁇ methoxytntyl-N 2 - ⁇ sobutyryl-2'-deoxyguanosme, or 5'- dimethoxyt ⁇ tylthymidine
- a prefe ⁇ ed method for production of ⁇ bonucleosides in the context of the present invention is to use a 5'-d ⁇ methoxyt ⁇ tyl protected nucleoside, with appropnate exocychc ammo protection, and no protecting groups on either of the 2'- or 3'- hydroxyl positions
- the linker can then react with either one of the two adjacent hydroxyl groups (it doesn't matter which) to give a mixture of 2'- and 3'- hnkages
- the unreacted hydroxyl groups may then be acetylated by treatment of the immobilized nucleoside with acetic anhyd ⁇ de
- ⁇ bonucleosides which have a 5'-d ⁇ methoxyt ⁇ tyl group, appropnate exocychc amino group protection, and either a 3'-hydroxyl protecting group or a mixture of 2'- and 3'- protecting groups can be used
- the 3'-protected compounds are generally unwanted
- Z— O— T [SUPPORT] may be produced by a process comprising the step of reacting together the compound of Formulae I and II:
- the reusable linker arm having the formula:
- activating group is intended to have a broad meaning and is intended to encompass electrophilic reagents capable of activating a carboxyl moiety (e.g., on the linking compound of Formula II) by attachment of a leaving group to the acyl carbon of the carboxl moiety - see, for example, M. Bodanszky, "Principles of Peptide Synthesis", Second Edition, Springer- Verlag, Berlin (1993), the contents of which are hereby incorporated by reference.
- the activating agent should be capable of initiating at least one of the following: (a) formation of a reactive acylating agent (this is an example of a derivate) from the carboxyl moeiy in a separate step or steps, followed by immediate treatment with the amino component (in this case, for example, an amino-terminated support) to form an amide linkage or a hydroxy component (in this case a hydroxy-terminated support or a hydroxyl group on the desired nucleoside) to form an ester linkage; (b) formation of an isolable acylating agent, separately, optionally with purification prior to treatment with the amino or hydroxy component as discussed in (a); and (c) formation of an acylating intermediate in the presence of the amino/ hydroxy component, by the addition of an activating agent to a mixture of the two components.
- a reactive acylating agent this is an example of a derivate
- the amino component in this case, for example, an amino-terminated support
- a hydroxy component
- the Letsinger method which first reacts oxalyl chloride with triazole, and then adds a nucleoside to the resulting oxalyl triazolide is an example of route (a).
- Conversion of the carboxylic acid group into an "active" ester using either p-nitrophenol, or di-, tri-, tetra-, or penta- chlorinated or fluorinated phenols, or N-hydrosuccinimide are common examples of route (b).
- the reaction of the compounds of Formulae I, II and III is conducted in the presence of a nucleophilic catalyst or additive (typically 4-dimethylamino pyridine (DMAP), 1-hydroxybenzotriazole (HOBt), or l-hydroxy-7-azabenzotriazole (HOAt)) to speed up the reaction and a tertiary amme base (typically tnethylamme, py ⁇ dine, or dusopropylethylamme) to ionize the carboxylic acid group
- a nucleophilic catalyst or additive typically 4-dimethylamino pyridine (DMAP), 1-hydroxybenzotriazole (HOBt), or l-hydroxy-7-azabenzotriazole (HOAt)
- DMAP 4-dimethylamino pyridine
- HABt 1-hydroxybenzotriazole
- HOAt l-hydroxy-7-azabenzotriazole
- the precise nature of the activation agent is not particularly restncted provided, of course, that the activated carboxylic acid group is capable of initiating formation of the ester or amide linkage, as appropriate, and the activating reagent does not have any delete ⁇ ous effect on the desired nucleoside
- an active ester I e , nitrophenyl, mtrophenylthio, tnchlorophenyl, t ⁇ fluorophenvl, pentachlorophenyl, pentafluorophenyl, or 3-hydroxv-2,3- d ⁇ hydro-4-oxo-benzot ⁇ azme esters
- an active hydroxylamine ester (1 e , N- hydroxyphthahmide or N-hydroxysuccimmide
- acid anhydride or mixed anhyd ⁇ de
- Non-limiting examples of actuating agents may be selected from the group consisting of arylsulfonyl chlo ⁇ des (e g , benzenesulfonyl chlo ⁇ de (BS- Cl), mesitvlenesulfonyl chlo ⁇ de (MS-C1), t ⁇ isopropylsulfonylchlo ⁇ de (TPS-C1)), active arylsulfonyl esters (I e , lmidazole, tnazole, nitrot ⁇ azole, or tetrazole esters ofBS-Cl.
- arylsulfonyl chlo ⁇ des e g , benzenesulfonyl chlo ⁇ de (BS- Cl)
- MS-C1 mesitvlenesulfonyl chlo ⁇ de
- TPS-C1 t ⁇ isopropylsulfonylchlo ⁇ de
- the order of reaction is not particularly rest ⁇ cted
- the compounds of Formulae I and III are initially reacted to form a conjugate which is reacted with the compound of Formula II
- the compounds of Formulae I and II are initially reacted to form a conjugate which is reacted with the compound of Formula III
- the capping reagent should be reversible so that the capping agent can be removed to regenerate the hydroxyl sites p ⁇ or to the next round of support de ⁇ vatization
- Capping of the unreacted sites is conventional and can be performed by reaction with an activated carboxylic acid or anhyd ⁇ de to form an ester, or by addition of a protecting group, as desc ⁇ bed hereinabove
- N-methyhmidazole in THF solution are useful examples of capping reagents
- DMT dimethoxyt ⁇ tyl
- B refers to a nucleobase as desc ⁇ bed hereinabove
- the support is recycled after oligonucleotide cleavage and support regeneration to a point in the reaction scheme where it may again be coupled with the HQPD-nucleoside conjugate for further oligonucleotide synthesis.
- Step #3 With further reference to "Oligo Synthesis” (Step #3) in Figure 2, once the present linker arm has been produced, it may be used in the conventional manner to synthesize an oligonucleotide - see, for example, United States patent 5,112,962 (Letsinger), incorporated by reference hereinabove. Once the oligonucleotide has been synthesized, it may be cleaved from the solid support to yield the free oligonucleotide and the support may then be regenerated - see Step #4 of Figure 2. The cleavage step comprises hydrolysis at the point of attachment of the initial nucleoside to the linking compound.
- the regeneration of the support involves the removal of two moieties: (i) the removal of the structure represented by Formula I (above) from Formula II (above), which occurs simultaneously with the release of the oligonucleotide product, and (ii) the removal of the moiety used to protect (cap) unreacted hydroxyl sites of Formula II (above) on the support. Removal of these two moieties can occur simultaneously or separately to regenerate the support. Simultaneous removal of both moieties using only a single reagent is simpler but care should be taken to use reagents which will not deleteriously affect the oligonucleotide product.
- a two-step regeneration involving the removal of the oligonucleotide using one reagent (typically ammonium hydroxide) and then treatment of the support with a second reagent (which may be faster but otherwise damaging to the oligonucleotide product thereby necessitating use of a two-step regeneration) allows flexibility in the choice of capping and regeneration reagents.
- the reagent used to effect cleavage is not particularly restricted and is within the purview of a person skilled in the art.
- the reagent is a base mild enough not to damage the oligonucleotide product but sufficiently strong to effect rapid cleavage.
- Non-limiting examples of suitable reagents for this purpose may be selected from the group consisting of ammonium hydroxide, ammonium hydroxide/methanol, ammonia/methanol, ammonium hydroxide/methylamine, potassium carbonate/methanol, t-butylamine, ethylenediamine, mefhylamine, dimethylamine, trimethylamine/water and the like. Cleavage may also be performed under neutral conditions using fluoride ion (i.e. 1M tetrabutylammonium fluoride/THF or triethylamine trihydro fluoride).
- the reagent used to remove the capping reagent from unreacted sites may consist of the above reagents or other stronger bases such as sodium or potassium hydroxide.
- ammonium hydroxide can be used to cleave the oligonucleotide product from the support, remove the HQPD linker arm, and cleave chloroacetyl protected hydroxyl groups in a single regeneration step.
- the prefe ⁇ ed temperature for the cleavage and regeneration is room temperature, but higher or lower temperatures can be employed, subject to the limitations of the apparatus used.
- LCAA Long chain alkylamine
- Gly glycerol
- CPG controlled pore glass
- Ammonium hydroxide solutions 28-30% and solvents were obtained from VWR Canlab (Edmonton, Alberta, Canada);
- Capping solutions were formulated as either Cap A (acetic anhydride/2, 6-lutidine/THF in a volume ratio of 1:1:8) and Cap B (N-methylimidazole and THF in a volume ratio of 16:84) or Cap A (chloroacetic anhydride and THF, 17% by weight) and Cap B (2, 6-lutidine and N-methylimidazole in THF in a volume ratio of 12:16:72); 7. Anhydrous pyridine and acetonitrile, distilled from CaH 2 ;
- DMAP 4-dimethylaminopyridine, reagent grade
- DEC l-(3-dimethylaminopropyl)-ethylcarbodiimide, reagent grade
- nucleoside (loading) on the insoluble supports was determined by spectrophotometric trityl analysis. In this procedure, a sample of support (4-5 mg) was accurately weighed directly into a 10 mL volumetric flask. A solution of dichloroacetic acid in 1 ,2-dichloroethane in a volume ration of 5:95 was then added to fill the flask. The contents were then thoroughly mixed and the absorbance of the orange coloured solution was measured at 503 nm using a Philips UV/Vis spectrophotometer. The nucleoside loading (in ⁇ mol/g of CPG) was then calculated as:
- a 503 absorbance at 503 nm
- Vol solution volume in mL
- Wt amount of CPG tested in mg. The accuracy of the trityl determination was approximately ⁇ 2-3%.
- Example 1 SYNTHESIS OF NUCLEOSIDE-3'-0-HODA HEMIESTERS 5'-Dimethoxytrityl-N-protected deoxyribonucleoside (10 mmol), hydroquinone-O, O'-diacetic acid (15 mmol, 3.39 g), 4-dimethylaminopyridine ( 1 mmol, 122 mg), and l-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride ( 15 mmol, 2.88 g) were combined in a 100 mL round bottom flask equipped with a magnetic stir bar. Triethylamine (0.8 mL) and anhydrous pyridine (50 mL) were added to the flask and the contents were sti ⁇ ed at room temperature overnight.
- Triethylamine 0.8 mL
- anhydrous pyridine 50 mL
- the reaction was checked by TLC (5% methanol/chloroform). If more than a trace of starting nucleoside was visible, more l-(3-dimethylaminopropyl)- 3-ethylcarbodiimide hydrochloride (2-5 mmol) was added to the reaction and stirring was continued for another day. When TLC showed complete disappearance of the starting nucleoside, the solution was concentrated by evaporation until a thick oil was formed. The oil was redissolved in chloroform ( ⁇ 200 mL) and transfer to a separatory funnel. The chloroform solution was washed with aqueous sodium bicarbonate ( ⁇ 100 mL x 2) and then water ( ⁇ 100 mL x 3).
- the funnel was slowly inverted to mix the two phases.
- the chloroform phase was collected and the aqueous phase was discarded. If an inseparable emulsion was formed, then either centrifugation (for small volumes) or (for large volumes) precipitation by addition of hexanes followed by filtration and redissolving the sticky precipitate back into chloroform can be performed.
- the chloroform solution was added to anhydrous magnesium sulfate and mixed to remove residual moisture from the solution.
- the magnesium sulfate was filtered off, the filtrated was washed with a small amount of chloroform and then the chloroform solution was evaporated to dryness.
- the hemiester sodium salt was converted into a more soluble pyridinium salt by dissolving the foam in pyridine ( ⁇ 50-100 mL) and then adding AG 50W- X4 W cation exchange resin (2 eq.). The mixture was sti ⁇ ed for approximately 5 minutes and then the ion exchange resin was filtered off. The pyridine solution was evaporated to dryness. A light brown foam formed and solidified. The sold was dried under vacuum overnight to remove excess pyridine.
- This example describes the synthesis of a C 12 linker arm within the scope of the present invention and how it can be used to convert commercially available amino-derivatized supports into reusable hydroxyl-derivatized supports.
- Example 3 - DERIVATIZATION OF TOYOPEARL HW-65F SUPPORT WITH 1.4-BUTANEDIOL DIGLYCIDYL ETHER This Example describes how hydroxyl surface groups on commercially available Toyopearl HW65 supports are extended with a butane diglycidyl linker to create a reusable support.
- Toyopearl HW-65F vinyl alcohol/methacrylic acid copolymer was obtained as a slurry in 500 ml 20% ethanol/water. This slurry was evaporated to dryness to yield of 90 g of dry support. The hydroxyl content of the dry support was determined, in triplicate, by derivatization with dimethoxytrityl chloride/tetrabutylammonium perchlorate and trityl analysis, to be 1 ,095 ⁇ mol/g.
- the epoxide loading was estimated to be 193 ⁇ mol/g.
- the epoxide denvatized support 25 g
- benzoic anhyd ⁇ de 51 g
- 4- dimethylammopyndine 6.6 g
- anhydrous pyndine 180 mL
- the support was filtered off, washed (methanol, then chloroform), and dned.
- Ports #1-4 dA Bz , dG lBu , dC Bz , and T phosphoramidites (0.2 M solutions).
- Port #10 28% Ammonium hydroxide.
- Port #11 1 M Chloroacetic anhydride in THF (Cap A reagent).
- Port #12 1 M 2,6-Lutidine and 2 M N-methylimidazole in THF (Cap B reagent).
- the synthesizer was then programmed to automatically execute the following steps:
- a "Begin" procedure consisting of a column wash, nucleoside coupling to the support by simultaneous addition (4.0 sec) of nucleoside hemiester (port #7) and coupling reagent (port #8) and a 600 sec wait, column wash, capping of unreacted hydroxyl sites (Cap A + B reagents, 300 sec), column wash, and priming of ports #1 , 2, 3, 4, and 9.
- the columns were removed from the synthesizer, manually treated with 0.05 M potassium carbonate/methanol solution (5 min), rinsed with methanol, dried by aspiration (5 min), re-installed on the synthesizer, and rinsed with anhydrous acetonitrile.
- the automated synthesis was then repeated (i.e., Steps 1, 2, and 3 above) using the same synthesis column a total of twelve times.
- the automated DNA synthesizer was set-up with reagents, as described in Example 4, with the exception of the Cap A and B reagents, which were as follows:
- Port #12 1 M N-Methylimidazole in acetonitrile (Cap B).
- the amount of trityl color released after the first detritylation step was collected and quantitated to determine the amount of nucleoside added to the support - the results are reported in Table 6.
- the released oligonucleotide solution was deprotected (55°C, 16 h), evaporated to removed ammonia, and quantitated by UV at 260 nm - the results are reported in Table 7.
- the composition of the products obtained in Table 7 was examined by gel electrophoresis and the expected products were obtained in each case. This indicated that methoxyacetic anhydride could also be used as a satisfactory capping reagent during the support recycling.
Abstract
Description
Claims
Priority Applications (4)
Application Number | Priority Date | Filing Date | Title |
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AU44940/99A AU4494099A (en) | 1998-07-02 | 1999-06-30 | Reusable solid support for oligonucleotide synthesis |
US09/720,907 US7135564B1 (en) | 1998-07-02 | 1999-06-30 | Reusable solid support for oligonucleotide synthesis |
JP2000558112A JP2002519433A (en) | 1998-07-02 | 1999-06-30 | Reusable solid support for oligonucleotide synthesis |
EP99927625A EP1091972A1 (en) | 1998-07-02 | 1999-06-30 | Reusable solid support for oligonucleotide synthesis |
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US9168398P | 1998-07-02 | 1998-07-02 | |
CA 2242649 CA2242649A1 (en) | 1998-07-02 | 1998-07-02 | Reusable solid support for oligonucleotide synthesis, process for production thereof and process for use thereof |
US60/091,683 | 1998-07-02 | ||
CA2,242,649 | 1998-07-02 |
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PCT/CA1999/000600 WO2000001711A1 (en) | 1998-07-02 | 1999-06-30 | Reusable solid support for oligonucleotide synthesis |
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JP (1) | JP2002519433A (en) |
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EP1347297A1 (en) * | 2000-12-28 | 2003-09-24 | Toyo Kohan Co., Ltd. | Method of reusing dna-immobilization substrate |
Citations (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO1992006103A1 (en) * | 1990-10-04 | 1992-04-16 | Imperial Chemical Industries Plc | Synthesis of oligonucleotides |
WO1993007883A1 (en) * | 1991-10-24 | 1993-04-29 | Isis Pharmaceuticals, Inc. | Derivatized oligonucleotides having improved uptake and other properties |
US5624711A (en) * | 1995-04-27 | 1997-04-29 | Affymax Technologies, N.V. | Derivatization of solid supports and methods for oligomer synthesis |
WO1997023496A1 (en) * | 1995-12-22 | 1997-07-03 | University Technologies International Inc. | Reusable solid support for oligonucleotide synthesis, process for production thereof and process for use thereof |
-
1999
- 1999-06-30 EP EP99927625A patent/EP1091972A1/en not_active Withdrawn
- 1999-06-30 JP JP2000558112A patent/JP2002519433A/en active Pending
- 1999-06-30 AU AU44940/99A patent/AU4494099A/en not_active Abandoned
- 1999-06-30 WO PCT/CA1999/000600 patent/WO2000001711A1/en not_active Application Discontinuation
Patent Citations (5)
Publication number | Priority date | Publication date | Assignee | Title |
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WO1992006103A1 (en) * | 1990-10-04 | 1992-04-16 | Imperial Chemical Industries Plc | Synthesis of oligonucleotides |
WO1993007883A1 (en) * | 1991-10-24 | 1993-04-29 | Isis Pharmaceuticals, Inc. | Derivatized oligonucleotides having improved uptake and other properties |
US5624711A (en) * | 1995-04-27 | 1997-04-29 | Affymax Technologies, N.V. | Derivatization of solid supports and methods for oligomer synthesis |
WO1997023496A1 (en) * | 1995-12-22 | 1997-07-03 | University Technologies International Inc. | Reusable solid support for oligonucleotide synthesis, process for production thereof and process for use thereof |
WO1997023497A1 (en) * | 1995-12-22 | 1997-07-03 | University Technologies International Inc. | Linker arm for solid support oligonucleotide synthesis and process for production thereof |
Non-Patent Citations (3)
Title |
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JAMES I W: "Linkers for Solid Phase Organic Synthesis", TETRAHEDRON, vol. 55, no. 16, 16 April 1999 (1999-04-16), pages 4855-4946, XP004161079, ISSN: 0040-4020 * |
PON R T ET AL: "Hydroquinone-O,O@?-Diacetic Acid As A More Labile Replacement For Succinic Acid Linkers in Solid-Phase Oligonucleotide Synthesis", TETRAHEDRON LETTERS, vol. 38, no. 19, 12 May 1997 (1997-05-12), pages 3327-3330, XP004061417, ISSN: 0040-4039 * |
PON R T ET AL: "Rapid Automated Derivatization of Solid-Phase Supports For Oligonucleotide Synthesis Using Uronium or Phosphonium Coupling Reagents", TETRAHEDRON LETTERS, vol. 38, no. 19, 12 May 1997 (1997-05-12), pages 3331-3334, XP004061418, ISSN: 0040-4039 * |
Cited By (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP1347297A1 (en) * | 2000-12-28 | 2003-09-24 | Toyo Kohan Co., Ltd. | Method of reusing dna-immobilization substrate |
EP1347297A4 (en) * | 2000-12-28 | 2007-06-06 | Toyo Kohan Co Ltd | Method of reusing dna-immobilization substrate |
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AU4494099A (en) | 2000-01-24 |
JP2002519433A (en) | 2002-07-02 |
EP1091972A1 (en) | 2001-04-18 |
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