EP1181301A1 - Oligonucleotide synthesis with lewis acids as activators - Google Patents
Oligonucleotide synthesis with lewis acids as activatorsInfo
- Publication number
- EP1181301A1 EP1181301A1 EP00926516A EP00926516A EP1181301A1 EP 1181301 A1 EP1181301 A1 EP 1181301A1 EP 00926516 A EP00926516 A EP 00926516A EP 00926516 A EP00926516 A EP 00926516A EP 1181301 A1 EP1181301 A1 EP 1181301A1
- Authority
- EP
- European Patent Office
- Prior art keywords
- group
- chloride
- composition according
- alkoxy
- magnesium
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Withdrawn
Links
- 239000002841 Lewis acid Substances 0.000 title claims abstract description 29
- 150000007517 lewis acids Chemical class 0.000 title claims abstract description 27
- 239000012190 activator Substances 0.000 title claims abstract description 14
- 238000002515 oligonucleotide synthesis Methods 0.000 title claims description 4
- 238000000034 method Methods 0.000 claims abstract description 20
- 150000008300 phosphoramidites Chemical class 0.000 claims abstract description 18
- 230000008569 process Effects 0.000 claims abstract description 13
- 108091034117 Oligonucleotide Proteins 0.000 claims abstract description 10
- -1 2-cyanoethoxy Chemical group 0.000 claims description 69
- 125000003545 alkoxy group Chemical group 0.000 claims description 18
- JUJWROOIHBZHMG-UHFFFAOYSA-N Pyridine Chemical compound C1=CC=NC=C1 JUJWROOIHBZHMG-UHFFFAOYSA-N 0.000 claims description 16
- WTEOIRVLGSZEPR-UHFFFAOYSA-N boron trifluoride Chemical compound FB(F)F WTEOIRVLGSZEPR-UHFFFAOYSA-N 0.000 claims description 16
- 239000000203 mixture Substances 0.000 claims description 16
- 125000000217 alkyl group Chemical group 0.000 claims description 14
- 229910052736 halogen Chemical group 0.000 claims description 13
- 150000002367 halogens Chemical group 0.000 claims description 13
- 229910015900 BF3 Inorganic materials 0.000 claims description 11
- TWRXJAOTZQYOKJ-UHFFFAOYSA-L Magnesium chloride Chemical compound [Mg+2].[Cl-].[Cl-] TWRXJAOTZQYOKJ-UHFFFAOYSA-L 0.000 claims description 10
- VSCWAEJMTAWNJL-UHFFFAOYSA-K aluminium trichloride Chemical compound Cl[Al](Cl)Cl VSCWAEJMTAWNJL-UHFFFAOYSA-K 0.000 claims description 10
- 125000004093 cyano group Chemical group *C#N 0.000 claims description 10
- 239000000543 intermediate Substances 0.000 claims description 10
- RBTARNINKXHZNM-UHFFFAOYSA-K iron trichloride Chemical compound Cl[Fe](Cl)Cl RBTARNINKXHZNM-UHFFFAOYSA-K 0.000 claims description 10
- VNDYJBBGRKZCSX-UHFFFAOYSA-L zinc bromide Chemical compound Br[Zn]Br VNDYJBBGRKZCSX-UHFFFAOYSA-L 0.000 claims description 10
- JIAARYAFYJHUJI-UHFFFAOYSA-L zinc dichloride Chemical compound [Cl-].[Cl-].[Zn+2] JIAARYAFYJHUJI-UHFFFAOYSA-L 0.000 claims description 10
- UMJSCPRVCHMLSP-UHFFFAOYSA-N pyridine Natural products COC1=CC=CN=C1 UMJSCPRVCHMLSP-UHFFFAOYSA-N 0.000 claims description 8
- 125000005159 cyanoalkoxy group Chemical group 0.000 claims description 7
- 239000000178 monomer Substances 0.000 claims description 7
- 239000002777 nucleoside Substances 0.000 claims description 7
- 125000005951 trifluoromethanesulfonyloxy group Chemical group 0.000 claims description 7
- 125000002103 4,4'-dimethoxytriphenylmethyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C(*)(C1=C([H])C([H])=C(OC([H])([H])[H])C([H])=C1[H])C1=C([H])C([H])=C(OC([H])([H])[H])C([H])=C1[H] 0.000 claims description 6
- 125000005196 alkyl carbonyloxy group Chemical group 0.000 claims description 6
- YCIMNLLNPGFGHC-UHFFFAOYSA-N catechol Chemical compound OC1=CC=CC=C1O YCIMNLLNPGFGHC-UHFFFAOYSA-N 0.000 claims description 6
- 150000001875 compounds Chemical class 0.000 claims description 6
- BHEPBYXIRTUNPN-UHFFFAOYSA-N hydridophosphorus(.) (triplet) Chemical compound [PH] BHEPBYXIRTUNPN-UHFFFAOYSA-N 0.000 claims description 6
- 229910052739 hydrogen Inorganic materials 0.000 claims description 6
- 239000001257 hydrogen Substances 0.000 claims description 6
- 229910021577 Iron(II) chloride Inorganic materials 0.000 claims description 5
- 229910021578 Iron(III) chloride Inorganic materials 0.000 claims description 5
- 229910021380 Manganese Chloride Inorganic materials 0.000 claims description 5
- GLFNIEUTAYBVOC-UHFFFAOYSA-L Manganese chloride Chemical compound Cl[Mn]Cl GLFNIEUTAYBVOC-UHFFFAOYSA-L 0.000 claims description 5
- JHXKRIRFYBPWGE-UHFFFAOYSA-K bismuth chloride Chemical compound Cl[Bi](Cl)Cl JHXKRIRFYBPWGE-UHFFFAOYSA-K 0.000 claims description 5
- 125000004438 haloalkoxy group Chemical group 0.000 claims description 5
- 125000004435 hydrogen atom Chemical group [H]* 0.000 claims description 5
- NMCUIPGRVMDVDB-UHFFFAOYSA-L iron dichloride Chemical compound Cl[Fe]Cl NMCUIPGRVMDVDB-UHFFFAOYSA-L 0.000 claims description 5
- OTCKOJUMXQWKQG-UHFFFAOYSA-L magnesium bromide Chemical compound [Mg+2].[Br-].[Br-] OTCKOJUMXQWKQG-UHFFFAOYSA-L 0.000 claims description 5
- 229910001623 magnesium bromide Inorganic materials 0.000 claims description 5
- 229910001629 magnesium chloride Inorganic materials 0.000 claims description 5
- BZQRBEVTLZHKEA-UHFFFAOYSA-L magnesium;trifluoromethanesulfonate Chemical compound [Mg+2].[O-]S(=O)(=O)C(F)(F)F.[O-]S(=O)(=O)C(F)(F)F BZQRBEVTLZHKEA-UHFFFAOYSA-L 0.000 claims description 5
- 235000002867 manganese chloride Nutrition 0.000 claims description 5
- 239000011565 manganese chloride Substances 0.000 claims description 5
- 229940102001 zinc bromide Drugs 0.000 claims description 5
- 235000005074 zinc chloride Nutrition 0.000 claims description 5
- 239000011592 zinc chloride Substances 0.000 claims description 5
- KDCGOANMDULRCW-UHFFFAOYSA-N 7H-purine Chemical compound N1=CNC2=NC=NC2=C1 KDCGOANMDULRCW-UHFFFAOYSA-N 0.000 claims description 4
- CZPWVGJYEJSRLH-UHFFFAOYSA-N Pyrimidine Chemical compound C1=CN=CN=C1 CZPWVGJYEJSRLH-UHFFFAOYSA-N 0.000 claims description 4
- 125000004430 oxygen atom Chemical group O* 0.000 claims description 4
- DUNKXUFBGCUVQW-UHFFFAOYSA-J zirconium tetrachloride Chemical compound Cl[Zr](Cl)(Cl)Cl DUNKXUFBGCUVQW-UHFFFAOYSA-J 0.000 claims description 4
- QCWXUUIWCKQGHC-UHFFFAOYSA-N Zirconium Chemical compound [Zr] QCWXUUIWCKQGHC-UHFFFAOYSA-N 0.000 claims description 3
- 125000001449 isopropyl group Chemical group [H]C([H])([H])C([H])(*)C([H])([H])[H] 0.000 claims description 3
- 238000002360 preparation method Methods 0.000 claims description 3
- 229910052726 zirconium Inorganic materials 0.000 claims description 3
- 125000005524 levulinyl group Chemical group 0.000 claims description 2
- 239000002243 precursor Substances 0.000 claims description 2
- XEEYBQQBJWHFJM-UHFFFAOYSA-N Iron Chemical compound [Fe] XEEYBQQBJWHFJM-UHFFFAOYSA-N 0.000 claims 4
- ZOXJGFHDIHLPTG-UHFFFAOYSA-N Boron Chemical compound [B] ZOXJGFHDIHLPTG-UHFFFAOYSA-N 0.000 claims 2
- FYYHWMGAXLPEAU-UHFFFAOYSA-N Magnesium Chemical compound [Mg] FYYHWMGAXLPEAU-UHFFFAOYSA-N 0.000 claims 2
- PXHVJJICTQNCMI-UHFFFAOYSA-N Nickel Chemical compound [Ni] PXHVJJICTQNCMI-UHFFFAOYSA-N 0.000 claims 2
- KDLHZDBZIXYQEI-UHFFFAOYSA-N Palladium Chemical compound [Pd] KDLHZDBZIXYQEI-UHFFFAOYSA-N 0.000 claims 2
- RTAQQCXQSZGOHL-UHFFFAOYSA-N Titanium Chemical compound [Ti] RTAQQCXQSZGOHL-UHFFFAOYSA-N 0.000 claims 2
- HCHKCACWOHOZIP-UHFFFAOYSA-N Zinc Chemical compound [Zn] HCHKCACWOHOZIP-UHFFFAOYSA-N 0.000 claims 2
- 229910052782 aluminium Inorganic materials 0.000 claims 2
- XAGFODPZIPBFFR-UHFFFAOYSA-N aluminium Chemical compound [Al] XAGFODPZIPBFFR-UHFFFAOYSA-N 0.000 claims 2
- 229910052797 bismuth Inorganic materials 0.000 claims 2
- JCXGWMGPZLAOME-UHFFFAOYSA-N bismuth atom Chemical compound [Bi] JCXGWMGPZLAOME-UHFFFAOYSA-N 0.000 claims 2
- 229910052796 boron Inorganic materials 0.000 claims 2
- 229910052742 iron Inorganic materials 0.000 claims 2
- 229910052749 magnesium Inorganic materials 0.000 claims 2
- 239000011777 magnesium Substances 0.000 claims 2
- WPBNNNQJVZRUHP-UHFFFAOYSA-L manganese(2+);methyl n-[[2-(methoxycarbonylcarbamothioylamino)phenyl]carbamothioyl]carbamate;n-[2-(sulfidocarbothioylamino)ethyl]carbamodithioate Chemical compound [Mn+2].[S-]C(=S)NCCNC([S-])=S.COC(=O)NC(=S)NC1=CC=CC=C1NC(=S)NC(=O)OC WPBNNNQJVZRUHP-UHFFFAOYSA-L 0.000 claims 2
- BASFCYQUMIYNBI-UHFFFAOYSA-N platinum Chemical compound [Pt] BASFCYQUMIYNBI-UHFFFAOYSA-N 0.000 claims 2
- 229910052719 titanium Inorganic materials 0.000 claims 2
- 239000010936 titanium Substances 0.000 claims 2
- 229910052725 zinc Inorganic materials 0.000 claims 2
- 239000011701 zinc Substances 0.000 claims 2
- VYZAMTAEIAYCRO-UHFFFAOYSA-N Chromium Chemical compound [Cr] VYZAMTAEIAYCRO-UHFFFAOYSA-N 0.000 claims 1
- RYGMFSIKBFXOCR-UHFFFAOYSA-N Copper Chemical compound [Cu] RYGMFSIKBFXOCR-UHFFFAOYSA-N 0.000 claims 1
- ZOKXTWBITQBERF-UHFFFAOYSA-N Molybdenum Chemical compound [Mo] ZOKXTWBITQBERF-UHFFFAOYSA-N 0.000 claims 1
- KJTLSVCANCCWHF-UHFFFAOYSA-N Ruthenium Chemical compound [Ru] KJTLSVCANCCWHF-UHFFFAOYSA-N 0.000 claims 1
- BQCADISMDOOEFD-UHFFFAOYSA-N Silver Chemical compound [Ag] BQCADISMDOOEFD-UHFFFAOYSA-N 0.000 claims 1
- ATJFFYVFTNAWJD-UHFFFAOYSA-N Tin Chemical compound [Sn] ATJFFYVFTNAWJD-UHFFFAOYSA-N 0.000 claims 1
- 229910052787 antimony Inorganic materials 0.000 claims 1
- WATWJIUSRGPENY-UHFFFAOYSA-N antimony atom Chemical compound [Sb] WATWJIUSRGPENY-UHFFFAOYSA-N 0.000 claims 1
- 125000003710 aryl alkyl group Chemical group 0.000 claims 1
- 229910052793 cadmium Inorganic materials 0.000 claims 1
- BDOSMKKIYDKNTQ-UHFFFAOYSA-N cadmium atom Chemical compound [Cd] BDOSMKKIYDKNTQ-UHFFFAOYSA-N 0.000 claims 1
- 229910052804 chromium Inorganic materials 0.000 claims 1
- 239000011651 chromium Substances 0.000 claims 1
- 229910017052 cobalt Inorganic materials 0.000 claims 1
- 239000010941 cobalt Substances 0.000 claims 1
- GUTLYIVDDKVIGB-UHFFFAOYSA-N cobalt atom Chemical compound [Co] GUTLYIVDDKVIGB-UHFFFAOYSA-N 0.000 claims 1
- 229910052802 copper Inorganic materials 0.000 claims 1
- 239000010949 copper Substances 0.000 claims 1
- PCHJSUWPFVWCPO-UHFFFAOYSA-N gold Chemical compound [Au] PCHJSUWPFVWCPO-UHFFFAOYSA-N 0.000 claims 1
- 229910052737 gold Inorganic materials 0.000 claims 1
- 239000010931 gold Substances 0.000 claims 1
- 229910052735 hafnium Inorganic materials 0.000 claims 1
- VBJZVLUMGGDVMO-UHFFFAOYSA-N hafnium atom Chemical compound [Hf] VBJZVLUMGGDVMO-UHFFFAOYSA-N 0.000 claims 1
- 229910052741 iridium Inorganic materials 0.000 claims 1
- GKOZUEZYRPOHIO-UHFFFAOYSA-N iridium atom Chemical compound [Ir] GKOZUEZYRPOHIO-UHFFFAOYSA-N 0.000 claims 1
- 229910052746 lanthanum Inorganic materials 0.000 claims 1
- FZLIPJUXYLNCLC-UHFFFAOYSA-N lanthanum atom Chemical compound [La] FZLIPJUXYLNCLC-UHFFFAOYSA-N 0.000 claims 1
- QSHDDOUJBYECFT-UHFFFAOYSA-N mercury Chemical compound [Hg] QSHDDOUJBYECFT-UHFFFAOYSA-N 0.000 claims 1
- 229910052753 mercury Inorganic materials 0.000 claims 1
- 229910052750 molybdenum Inorganic materials 0.000 claims 1
- 239000011733 molybdenum Substances 0.000 claims 1
- 229910052759 nickel Inorganic materials 0.000 claims 1
- 229910052758 niobium Inorganic materials 0.000 claims 1
- 239000010955 niobium Substances 0.000 claims 1
- GUCVJGMIXFAOAE-UHFFFAOYSA-N niobium atom Chemical compound [Nb] GUCVJGMIXFAOAE-UHFFFAOYSA-N 0.000 claims 1
- 229910052762 osmium Inorganic materials 0.000 claims 1
- SYQBFIAQOQZEGI-UHFFFAOYSA-N osmium atom Chemical compound [Os] SYQBFIAQOQZEGI-UHFFFAOYSA-N 0.000 claims 1
- 229910052763 palladium Inorganic materials 0.000 claims 1
- 229910052697 platinum Inorganic materials 0.000 claims 1
- 229910052702 rhenium Inorganic materials 0.000 claims 1
- WUAPFZMCVAUBPE-UHFFFAOYSA-N rhenium atom Chemical compound [Re] WUAPFZMCVAUBPE-UHFFFAOYSA-N 0.000 claims 1
- 229910052707 ruthenium Inorganic materials 0.000 claims 1
- 229910052706 scandium Inorganic materials 0.000 claims 1
- SIXSYDAISGFNSX-UHFFFAOYSA-N scandium atom Chemical compound [Sc] SIXSYDAISGFNSX-UHFFFAOYSA-N 0.000 claims 1
- 229910052709 silver Inorganic materials 0.000 claims 1
- 239000004332 silver Substances 0.000 claims 1
- 229910052715 tantalum Inorganic materials 0.000 claims 1
- GUVRBAGPIYLISA-UHFFFAOYSA-N tantalum atom Chemical compound [Ta] GUVRBAGPIYLISA-UHFFFAOYSA-N 0.000 claims 1
- 229910052714 tellurium Inorganic materials 0.000 claims 1
- PORWMNRCUJJQNO-UHFFFAOYSA-N tellurium atom Chemical compound [Te] PORWMNRCUJJQNO-UHFFFAOYSA-N 0.000 claims 1
- 229910052718 tin Inorganic materials 0.000 claims 1
- 239000011135 tin Substances 0.000 claims 1
- WFKWXMTUELFFGS-UHFFFAOYSA-N tungsten Chemical compound [W] WFKWXMTUELFFGS-UHFFFAOYSA-N 0.000 claims 1
- 229910052721 tungsten Inorganic materials 0.000 claims 1
- 239000010937 tungsten Substances 0.000 claims 1
- 229910052720 vanadium Inorganic materials 0.000 claims 1
- GPPXJZIENCGNKB-UHFFFAOYSA-N vanadium Chemical compound [V]#[V] GPPXJZIENCGNKB-UHFFFAOYSA-N 0.000 claims 1
- 229910052727 yttrium Inorganic materials 0.000 claims 1
- VWQVUPCCIRVNHF-UHFFFAOYSA-N yttrium atom Chemical compound [Y] VWQVUPCCIRVNHF-UHFFFAOYSA-N 0.000 claims 1
- 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 abstract description 6
- 230000015572 biosynthetic process Effects 0.000 abstract description 5
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- 230000004913 activation Effects 0.000 description 6
- 125000003118 aryl group Chemical group 0.000 description 6
- 235000019439 ethyl acetate Nutrition 0.000 description 6
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- 229910000030 sodium bicarbonate Inorganic materials 0.000 description 5
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- 238000004809 thin layer chromatography Methods 0.000 description 4
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- 125000002777 acetyl group Chemical group [H]C([H])([H])C(*)=O 0.000 description 3
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- 125000003277 amino group Chemical group 0.000 description 3
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- 231100000647 material safety data sheet Toxicity 0.000 description 3
- 239000002904 solvent Substances 0.000 description 3
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- 230000002378 acidificating effect Effects 0.000 description 2
- 125000002102 aryl alkyloxo group Chemical group 0.000 description 2
- CUFNKYGDVFVPHO-UHFFFAOYSA-N azulene Chemical compound C1=CC=CC2=CC=CC2=C1 CUFNKYGDVFVPHO-UHFFFAOYSA-N 0.000 description 2
- 125000001797 benzyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C([H])([H])* 0.000 description 2
- 125000001584 benzyloxycarbonyl group Chemical group C(=O)(OCC1=CC=CC=C1)* 0.000 description 2
- 125000004432 carbon atom Chemical group C* 0.000 description 2
- 229940104302 cytosine Drugs 0.000 description 2
- YMWUJEATGCHHMB-DICFDUPASA-N dichloromethane-d2 Chemical compound [2H]C([2H])(Cl)Cl YMWUJEATGCHHMB-DICFDUPASA-N 0.000 description 2
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 2
- 239000000463 material Substances 0.000 description 2
- WWZKQHOCKIZLMA-UHFFFAOYSA-N octanoic acid Chemical compound CCCCCCCC(O)=O WWZKQHOCKIZLMA-UHFFFAOYSA-N 0.000 description 2
- 150000007530 organic bases Chemical class 0.000 description 2
- 239000012044 organic layer Substances 0.000 description 2
- 125000003170 phenylsulfonyl group Chemical group C1(=CC=CC=C1)S(=O)(=O)* 0.000 description 2
- 238000012163 sequencing technique Methods 0.000 description 2
- 239000007787 solid Substances 0.000 description 2
- 238000010532 solid phase synthesis reaction Methods 0.000 description 2
- 241000894007 species Species 0.000 description 2
- 125000000999 tert-butyl group Chemical group [H]C([H])([H])C(*)(C([H])([H])[H])C([H])([H])[H] 0.000 description 2
- RWQNBRDOKXIBIV-UHFFFAOYSA-N thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 description 2
- 125000001889 triflyl group Chemical group FC(F)(F)S(*)(=O)=O 0.000 description 2
- 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 description 2
- HEVMDQBCAHEHDY-UHFFFAOYSA-N (Dimethoxymethyl)benzene Chemical compound COC(OC)C1=CC=CC=C1 HEVMDQBCAHEHDY-UHFFFAOYSA-N 0.000 description 1
- JPRPJUMQRZTTED-UHFFFAOYSA-N 1,3-dioxolanyl Chemical group [CH]1OCCO1 JPRPJUMQRZTTED-UHFFFAOYSA-N 0.000 description 1
- MCTWTZJPVLRJOU-UHFFFAOYSA-N 1-methyl-1H-imidazole Chemical compound CN1C=CN=C1 MCTWTZJPVLRJOU-UHFFFAOYSA-N 0.000 description 1
- YBYIRNPNPLQARY-UHFFFAOYSA-N 1H-indene Natural products C1=CC=C2CC=CC2=C1 YBYIRNPNPLQARY-UHFFFAOYSA-N 0.000 description 1
- 125000004797 2,2,2-trichloroethoxy group Chemical group ClC(CO*)(Cl)Cl 0.000 description 1
- 125000000453 2,2,2-trichloroethyl group Chemical group [H]C([H])(*)C(Cl)(Cl)Cl 0.000 description 1
- YQTCQNIPQMJNTI-UHFFFAOYSA-N 2,2-dimethylpropan-1-one Chemical group CC(C)(C)[C]=O YQTCQNIPQMJNTI-UHFFFAOYSA-N 0.000 description 1
- HUHXLHLWASNVDB-UHFFFAOYSA-N 2-(oxan-2-yloxy)oxane Chemical class O1CCCCC1OC1OCCCC1 HUHXLHLWASNVDB-UHFFFAOYSA-N 0.000 description 1
- 125000003821 2-(trimethylsilyl)ethoxymethyl group Chemical group [H]C([H])([H])[Si](C([H])([H])[H])(C([H])([H])[H])C([H])([H])C(OC([H])([H])[*])([H])[H] 0.000 description 1
- 125000004777 2-fluoroethyl group Chemical group [H]C([H])(F)C([H])([H])* 0.000 description 1
- QSIFOTQDNVCTTM-UHFFFAOYSA-N 3-methyl-1h-imidazol-3-ium;trifluoromethanesulfonate Chemical compound CN1C=CN=C1.OS(=O)(=O)C(F)(F)F QSIFOTQDNVCTTM-UHFFFAOYSA-N 0.000 description 1
- 238000004679 31P NMR spectroscopy Methods 0.000 description 1
- 229960000549 4-dimethylaminophenol Drugs 0.000 description 1
- FOEPLOQMUWYHBM-UHFFFAOYSA-N 5-(trifluoromethyl)-2h-tetrazole Chemical compound FC(F)(F)C=1N=NNN=1 FOEPLOQMUWYHBM-UHFFFAOYSA-N 0.000 description 1
- GONFBOIJNUKKST-UHFFFAOYSA-N 5-ethylsulfanyl-2h-tetrazole Chemical compound CCSC=1N=NNN=1 GONFBOIJNUKKST-UHFFFAOYSA-N 0.000 description 1
- MGISCGVZJJIDSR-UHFFFAOYSA-N 7h-purin-6-amine Chemical compound NC1=NC=NC2=C1NC=N2.NC1=NC=NC2=C1NC=N2 MGISCGVZJJIDSR-UHFFFAOYSA-N 0.000 description 1
- 229930024421 Adenine Natural products 0.000 description 1
- GFFGJBXGBJISGV-UHFFFAOYSA-N Adenine Chemical compound NC1=NC=NC2=C1N=CN2 GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 description 1
- QWOJMRHUQHTCJG-UHFFFAOYSA-N CC([CH2-])=O Chemical compound CC([CH2-])=O QWOJMRHUQHTCJG-UHFFFAOYSA-N 0.000 description 1
- 239000004215 Carbon black (E152) Substances 0.000 description 1
- VEXZGXHMUGYJMC-UHFFFAOYSA-M Chloride anion Chemical compound [Cl-] VEXZGXHMUGYJMC-UHFFFAOYSA-M 0.000 description 1
- UFHFLCQGNIYNRP-UHFFFAOYSA-N Hydrogen Chemical compound [H][H] UFHFLCQGNIYNRP-UHFFFAOYSA-N 0.000 description 1
- BAVYZALUXZFZLV-UHFFFAOYSA-N Methylamine Chemical compound NC BAVYZALUXZFZLV-UHFFFAOYSA-N 0.000 description 1
- WPPONCHFOIIFIJ-UHFFFAOYSA-N N1N=NN=[C-]1 Chemical compound N1N=NN=[C-]1 WPPONCHFOIIFIJ-UHFFFAOYSA-N 0.000 description 1
- 238000005481 NMR spectroscopy Methods 0.000 description 1
- 229910019142 PO4 Inorganic materials 0.000 description 1
- UIIMBOGNXHQVGW-DEQYMQKBSA-M Sodium bicarbonate-14C Chemical compound [Na+].O[14C]([O-])=O UIIMBOGNXHQVGW-DEQYMQKBSA-M 0.000 description 1
- DHKHKXVYLBGOIT-UHFFFAOYSA-N acetaldehyde Diethyl Acetal Natural products CCOC(C)OCC DHKHKXVYLBGOIT-UHFFFAOYSA-N 0.000 description 1
- 229960000643 adenine Drugs 0.000 description 1
- OBETXYAYXDNJHR-UHFFFAOYSA-N alpha-ethylcaproic acid Natural products CCCCC(CC)C(O)=O OBETXYAYXDNJHR-UHFFFAOYSA-N 0.000 description 1
- 150000001412 amines Chemical class 0.000 description 1
- 235000011114 ammonium hydroxide Nutrition 0.000 description 1
- 125000003785 benzimidazolyl group Chemical group N1=C(NC2=C1C=CC=C2)* 0.000 description 1
- 125000003236 benzoyl group Chemical group [H]C1=C([H])C([H])=C(C([H])=C1[H])C(*)=O 0.000 description 1
- 239000013626 chemical specie Substances 0.000 description 1
- 239000003795 chemical substances by application Substances 0.000 description 1
- 125000004218 chloromethyl group Chemical group [H]C([H])(Cl)* 0.000 description 1
- 150000005676 cyclic carbonates Chemical class 0.000 description 1
- 125000004122 cyclic group Chemical group 0.000 description 1
- 238000000354 decomposition reaction Methods 0.000 description 1
- 229940043279 diisopropylamine Drugs 0.000 description 1
- KPUWHANPEXNPJT-UHFFFAOYSA-N disiloxane Chemical class [SiH3]O[SiH3] KPUWHANPEXNPJT-UHFFFAOYSA-N 0.000 description 1
- 125000001495 ethyl group Chemical group [H]C([H])([H])C([H])([H])* 0.000 description 1
- 125000004672 ethylcarbonyl group Chemical group [H]C([H])([H])C([H])([H])C(*)=O 0.000 description 1
- 125000006125 ethylsulfonyl group Chemical group 0.000 description 1
- 238000004880 explosion Methods 0.000 description 1
- 125000002485 formyl group Chemical group [H]C(*)=O 0.000 description 1
- 125000001475 halogen functional group Chemical group 0.000 description 1
- 150000004677 hydrates Chemical class 0.000 description 1
- 229930195733 hydrocarbon Natural products 0.000 description 1
- 150000002430 hydrocarbons Chemical class 0.000 description 1
- 125000002887 hydroxy group Chemical group [H]O* 0.000 description 1
- 239000012535 impurity Substances 0.000 description 1
- 125000003392 indanyl group Chemical group C1(CCC2=CC=CC=C12)* 0.000 description 1
- 125000003454 indenyl group Chemical group C1(C=CC2=CC=CC=C12)* 0.000 description 1
- 125000000959 isobutyl group Chemical group [H]C([H])([H])C([H])(C([H])([H])[H])C([H])([H])* 0.000 description 1
- 230000007246 mechanism Effects 0.000 description 1
- 125000004184 methoxymethyl group Chemical group [H]C([H])([H])OC([H])([H])* 0.000 description 1
- 150000005217 methyl ethers Chemical class 0.000 description 1
- 125000002496 methyl group Chemical group [H]C([H])([H])* 0.000 description 1
- QNJMDPIFQZSNPZ-UHFFFAOYSA-N methyl(phenyl)azanium;2,2,2-trichloroacetate Chemical compound [O-]C(=O)C(Cl)(Cl)Cl.C[NH2+]C1=CC=CC=C1 QNJMDPIFQZSNPZ-UHFFFAOYSA-N 0.000 description 1
- 125000004170 methylsulfonyl group Chemical group [H]C([H])([H])S(*)(=O)=O 0.000 description 1
- PSHKMPUSSFXUIA-UHFFFAOYSA-N n,n-dimethylpyridin-2-amine Chemical compound CN(C)C1=CC=CC=N1 PSHKMPUSSFXUIA-UHFFFAOYSA-N 0.000 description 1
- 125000004108 n-butyl group Chemical group [H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])* 0.000 description 1
- TXXJGCVOHDSYBC-UHFFFAOYSA-N n-methylaniline;2,2,2-trifluoroacetic acid Chemical compound [O-]C(=O)C(F)(F)F.C[NH2+]C1=CC=CC=C1 TXXJGCVOHDSYBC-UHFFFAOYSA-N 0.000 description 1
- 125000000740 n-pentyl group Chemical group [H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])* 0.000 description 1
- RRTXKQSFZYOTNW-UHFFFAOYSA-N n-phosphanyl-n-propan-2-ylpropan-2-amine Chemical group CC(C)N(P)C(C)C RRTXKQSFZYOTNW-UHFFFAOYSA-N 0.000 description 1
- 125000004123 n-propyl group Chemical group [H]C([H])([H])C([H])([H])C([H])([H])* 0.000 description 1
- 125000001624 naphthyl group Chemical group 0.000 description 1
- 125000005146 naphthylsulfonyl group Chemical group C1(=CC=CC2=CC=CC=C12)S(=O)(=O)* 0.000 description 1
- 125000000449 nitro group Chemical group [O-][N+](*)=O 0.000 description 1
- 229910052757 nitrogen Inorganic materials 0.000 description 1
- 125000003835 nucleoside group Chemical group 0.000 description 1
- 239000002773 nucleotide Substances 0.000 description 1
- 125000003729 nucleotide group Chemical group 0.000 description 1
- 125000006340 pentafluoro ethyl group Chemical group FC(F)(F)C(F)(F)* 0.000 description 1
- 125000001997 phenyl group Chemical group [H]C1=C([H])C([H])=C(*)C([H])=C1[H] 0.000 description 1
- UYWQUFXKFGHYNT-UHFFFAOYSA-N phenylmethyl ester of formic acid Natural products O=COCC1=CC=CC=C1 UYWQUFXKFGHYNT-UHFFFAOYSA-N 0.000 description 1
- NBIIXXVUZAFLBC-UHFFFAOYSA-K phosphate Chemical compound [O-]P([O-])([O-])=O NBIIXXVUZAFLBC-UHFFFAOYSA-K 0.000 description 1
- 239000010452 phosphate Substances 0.000 description 1
- SXADIBFZNXBEGI-UHFFFAOYSA-N phosphoramidous acid Chemical group NP(O)O SXADIBFZNXBEGI-UHFFFAOYSA-N 0.000 description 1
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 1
- 125000006239 protecting group Chemical group 0.000 description 1
- 229920006395 saturated elastomer Polymers 0.000 description 1
- 125000002914 sec-butyl group Chemical group [H]C([H])([H])C([H])([H])C([H])(*)C([H])([H])[H] 0.000 description 1
- 150000003335 secondary amines Chemical group 0.000 description 1
- 235000011152 sodium sulphate Nutrition 0.000 description 1
- 125000001424 substituent group Chemical group 0.000 description 1
- 238000010189 synthetic method Methods 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
- 125000001712 tetrahydronaphthyl group Chemical group C1(CCCC2=CC=CC=C12)* 0.000 description 1
- 229940113082 thymine Drugs 0.000 description 1
- 230000001052 transient effect Effects 0.000 description 1
- 125000000876 trifluoromethoxy group Chemical group FC(F)(F)O* 0.000 description 1
- 239000013638 trimer Substances 0.000 description 1
- 125000000026 trimethylsilyl group Chemical group [H]C([H])([H])[Si]([*])(C([H])([H])[H])C([H])([H])[H] 0.000 description 1
- 229940035893 uracil Drugs 0.000 description 1
- 125000001834 xanthenyl group Chemical group C1=CC=CC=2OC3=CC=CC=C3C(C12)* 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
- C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
- C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
- C07H19/06—Pyrimidine radicals
- C07H19/10—Pyrimidine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
- C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
- C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
- C07H19/16—Purine radicals
- C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
-
- 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 process utilizing Lewis acids as activators in the preparation of oligonucleotides by phosphoramidite chemistry.
- the present invention relates generally to the fields of organic chemistry and biology.
- the present invention is directed to compositions and methods for use in oligonucleotide synthesis.
- Phosphoramidite chemistry (Beaucage, S. L., and Lyer, R. P. Tetrahedron (1992), 48, 2223-2311) has become by far the most widely used coupling chemistry for the synthesis of oligonucleotides.
- phosphoramidite synthesis of oligonucleotides involves activation of nucleoside phosphoramidite monomer precursors by reaction with an activating agent to form activated intermediates, followed by sequential addition of the activated intermediates to the growing oligonucleotide chain (generally anchored at one end to a suitable solid support) to form the oligonucleotide product.
- Tetrazole is commonly used for the activation of the nucleoside phosphoramidite monomers; the activation occurs by the mechanism depicted in Scheme I.
- Tetrazole has an acidic proton which presumably protonates the basic nitrogen of the diisopropylamino phosphine group, thus making the diisopropylamino group a leaving group.
- the negatively charged tetrazolium ion then makes an attack on the trivalent phosphorous, forming a transient phosphorous tetrazolide species.
- the 5'-OH group of the solid support bound nucleoside then attacks the active trivalent phosphorous species, resulting in the formation of the internucleotide linkage.
- tetrazole Principal drawbacks of tetrazole are its cost and instability which includes its potential to explode (Material Safety Data Sheets or MSDS lists IH-tetrazole as a severe explosion hazard). Because of its inherent instability, sublimed tetrazole is generally required to ensure desired coupling yields. Further, tetrazole (which is typically used near its saturated solubility of 0.5M) tends to precipitate out of acetonitrile solution at cold temperatures; this can lead to valve blockage on some automated DNA synthesizers. Other activators which work almost as efficiently as tetrazole have similar drawbacks to those of tetrazole as discussed above.
- activators which are all proton donors, include the following members of the tetrazole class of activators: 5-(p- nitrophenyl) tetrazole (Froehler, B. C. and Mattcucci, M. D., Tetrahedron Letters (1983), 24, 3171-3174); 5-(p-nitrophenyl) tetrazole and DMAP (Pon, R.T., Tetrahedron Letters (1987), 28, 3643-3646); and 5-(ethylthio)- IH-tetrazole (Wright, P. et al., Tetrahedron
- a 1 :1 mixture of benzimidazole and BF 3 etherate is disclosed wherein the BF 3 component acts to increase the acidity of the benzimidazole proton necessary for activation of the phosphoramidite (intermediates).
- the benzimidazole BF 3 complex acts in a manner similar to tetrazole described in Scheme 1.
- the present invention does not activate phosphoramidite intermediates with a proton donor but instead utilizes Lewis acids for activation.
- BF 3 etherate is used in the present invention.
- the advantages of BF 3 etherate over the benzimidazole BF 3 complex include commercial availability and ease of removal of diethyl ether versus removal of benzimidazole.
- the activated phosphoramidite intermediates are highly sensitive to moisture. An excess of 50% to 100% of the highly valuable phosphoramidites are required for sequencing even with anhydrous solvents ( ⁇ 20 ppm moisture content). The presence of trace amounts of moisture results in considerable loss of yield and an increase in deleted sequencing impurities.
- Lewis acids can act as moisture scavengers minimizing decomposition of the phosphoramidite. Therefore, the use of Lewis acids for activation of phosphoramidite intermediates leads to improved coupling efficiency, lower cost, and convenient material handling and operation.
- B 1 is selected from the group consisting of a purine base and a pyrimidine base;
- R 1 is a secondary amine, a preferred amine is diisopropylamine;
- R 2 is selected from the group consisting of alkoxy, alkyl, alkylsulfonylalkoxy arylsulfonylalkoxy, cyanoalkoxy, and haloalkoxy;
- R 3 is a hydroxy-protecting group, a preferred group is 4-4'-dimethoxytrityl
- R 4 is selected from the group consisting of hydrogen and -OR 7 wherein, R 7 is a hydroxy- protecting group; comprising treating the phosphoramidite monomers of formula I with an optional amount of pyridine and a Lewis acid, preferred Lewis acids are selected from aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride and zirconium(IN) chloride.
- preferred Lewis acids are selected from aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride and zirconium(IN) chloride.
- alkoxy refers to an alkyl group, as defined herein, appended to the parent molecular moiety through an oxy group, as defined herein.
- alkoxy include, but are not limited to, methoxy, ethoxy, propoxy, 2-propoxy, butoxy, tert-butoxy, pentyloxy, and the like.
- alkyl refers to a straight or branched chain hydrocarbon containing from 1 to 5 carbon atoms.
- Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl, iso-butyl, tert-butyl, n-pentyl, and the like.
- alkylcarbonyl refers to an alkyl group, as defined herein, appended to the parent molecular moiety through a carbonyl group, as defined herein.
- Representative examples of alkylcarbonyl include, but are not limited to, acetyl, ethylcarbonyl, and the like.
- alkylcarbonyloxy refers to an alkylcarbonyl group, as defined herein, appended to the parent molecular moiety through an oxy group, as defined herein.
- Representative examples of alkylcarbonyloxy include, but are not limited to, acetyloxy, ethylcarbonyloxy, t-butylcarbonyloxy, and the like.
- alkylsulfonyl refers to an alkyl group, as defined herein, appended to the parent molecular moiety through a sulfonyl group, as defined herein.
- Representative examples of alkylsulfonyl include, but are not limited to, methylsulfonyl, ethylsulfonyl, and the like.
- alkylsulfonylalkoxy refers to an alkylsulfonyl group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein.
- Representative examples of alkylsulfonylalkoxy include, but are not limited to, 2-methylsulfonylethoxy, 2-ethylsulfonylethoxy, and the like.
- amino refers to a -NH 2 group.
- amino-protecting group or “N-protecting group,” refer to groups intended to protect an amino group against undersirable reactions during synthetic procedures. Commonly used nitrogen-protecting groups are disclosed in Greene, T. W., &
- nitrogen-protecting groups are formyl, acetyl, benzoyl, pivaloyl, t-butylacetyl, phenylsulfonyl, benzyl, t-butyloxycarbonyl (Boc), and benzyloxycarbonyl (Cbz).
- aryl refers to an aromatic monocyclic ring system, or a bicyclic-fused ring system wherein one or both of the fused rings are aromatic.
- aryl include, but are not limited to, azulene, indanyl, indenyl, naphthyl, phenyl, tetrahydronaphthyl, and the like.
- the aryl groups of this invention can be substituted with 1, 2, or 3 substituents independently selected from alkyl, cyano, halogen, haloalkyl, and nitro.
- arylalkoxy refers to an aryl group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein.
- arylalkoxy include, but are not limited to, 2-phenylethoxy, 2-naphthylethoxy, 2-(4-nitrophenyl)ethoxy, and the like.
- arylsulfonyl refers to an aryl group, as defined herein, appended to the parent molecular moiety through a sulfonyl group, as defined herein.
- arylsulfonyl include, but are not limited to, phenylsulfonyl, naphthylsulfonyl, and the like.
- arylsulfonylalkoxy refers to an arylsulfonyl group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein.
- Representative examples of arylsulfonylalkoxy include, but are not limited to, 2-phenylsulfonylethoxy, 3-phenylsulfonylpropoxy, and the like.
- carbonyl refers to a -C(O)- group.
- catechol refers to a C 6 H 4 - 1 ,2-(O-) 2 group, wherein both oxygen atoms are attached to M, as defined herein.
- cyano refers to a -CN group.
- cyanoalkoxy refers to a cyano group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein.
- Representative examples of cyanoalkoxy include, but are not limited to, 2-cyanoethoxy, 3-cyanopropoxy, 1 -methyl-2-cyanoethoxy, l,l-dimethyl-2-cyanoethoxy, and the like.
- halo refers to -Cl, -Br, -I or -F.
- haloalkoxy refers to at least one halogen, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein. Representative examples of haloalkoxy include, but are not limited to, 2,2,2- trichloroethoxy, l,l-dimethyl-2,2,2-trichloroethoxy, trifluoromethoxy, and the like.
- haloalkyl refers to at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
- Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2- fluoroethyl, trifiuoromethyl, pentafluoroethyl, 2-chloro-3-fluoropentyl, and the like.
- hydroxy-protecting group or "O-protecting group” refers to groups intended to protect a hydroxy group against undesirable reactions during synthetic procedures. Commonly used hydroxy-protecting groups are disclosed in T.H. Greene and P.G.M. Wuts, Protective Groups in Organic Synthesis. 2nd edition, John Wiley & Sons, New York (1991), which is hereby incorporated by reference.
- hydroxy- protecting groups include, but are not limited to, substituted methyl ethers, for example, methoxymethyl, benzyloxymethyl, 2-methoxyethoxymethyl, 2-(trimethylsilyl)- ethoxymethyl, benzyl, and triphenylmethyl; tetrahydropyranyl ethers; substituted ethyl ethers, for example, 2,2,2-trichloroethyl and t-butyl; silyl ethers, for example, trimethylsilyl, t-butyldimethylsilyl and t-butyldiphenylsilyl; cyclic acetals and ketals, for example, methylene acetal, acetonide and benzylidene acetal; cyclic ortho esters, for example, methoxymethylene; cyclic carbonates; cyclic boronates; carbonyl derivatives, for example, acetyl, p-phenylazopheny
- Lewis acid refers to a chemical species, other than a proton, that has a vacant orbital or accepts an electron pair. It is to be understood that Lewis acids can be purchased or prepared as complexes including but not limited to, etherates, hydrates, and thioetherates. It is to be further understood that complexes purchased or prepared for the present invention do not contain an acidic proton.
- Lewis acid examples include, but are not limited to, aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride, zirconium(IV) chloride, and the like.
- methylenedioxy refers to a -OC(R 80 )(R 81 )O- group wherein R 80 and R 81 are independently selected from hydrogen and alkyl. The oxygen atoms of the methylenedioxy group are attached to the parent molecular moiety through two adjacent carbon atoms.
- methylenedioxy group examples include, but are not limited to, 1,3-dioxolanyl, 2,2-dimethyl-l,3-dioxolanyl, 2-methyl-l,3- dioxolanyl, and the like.
- purine base refers to an organic base selected from 9H-purin-6-ylamine (adenine) and 2-amino-l,9-dihydro-6H-purin-6-one (guanine).
- adenine 9H-purin-6-ylamine
- guanine 2-amino-l,9-dihydro-6H-purin-6-one
- the amino group attached to adenine can be protected with a nitrogen-protecting group.
- proto refers to H + .
- pyrimidine base refers to an organic base selected from 2,4(lH,3H)-pyrimidinedione (uracil), 5-methyl-2,4(lH,3H)-pyrimidinedione (thymine), and 4-amino-2(lH)-pyrimidinone (cytosine).
- uracil 2,4(lH,3H)-pyrimidinedione
- thymine 5-methyl-2,4(lH,3H)-pyrimidinedione
- cytosine 4-amino-2(lH)-pyrimidinone
- the amino group attached to cytosine can be protected with a nitrogen-protecting group.
- sulfonyl refers to a -SO 2 - group.
- trifluoromethane refers to a -CF 3 group.
- trifluoromethanesulfonyl refers to a trifluoromethane group, as defined herein, appended to the parent molecular moiety through a sulfonyl group, as defined herein.
- trifluoromethanesulfonyloxy refers to a trifluoromethanesulfonyl group, as defined herein, appended to the parent molecular moiety through an oxy group, as defined herein.
- dimer (iii) can be oxidizied using standard conditions know to those of ordinary skill in the art to give the phosphate, (J. Am. Chem. Soc, (1976), 98, 3655-3661).
- the 5'-OH of the oxidized dimer can be deprotected and treated with a Lewis acid activated phophoramidite monomer to form a trimer. This sequence of steps can be repeated until an oligonucleotide of desired length has been synthesized such that the process of the present invention can be used for preparing oligonucleotides, including solid phase synthesis thereof.
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Abstract
A process for synthesizing oligonucleotides by phosphoramidite chemistry wherein the improvement is the use of Lewis acids as activators for formation of the phosphorous-oxygen bond.
Description
OLIGONUCLEOTIDE SYNTHESIS WITH LEWIS ACIDS AS ACTIVATORS
Technical Field
The present invention relates to a process utilizing Lewis acids as activators in the preparation of oligonucleotides by phosphoramidite chemistry.
Background of the Invention
The present invention relates generally to the fields of organic chemistry and biology. In particular, the present invention is directed to compositions and methods for use in oligonucleotide synthesis.
Phosphoramidite chemistry (Beaucage, S. L., and Lyer, R. P. Tetrahedron (1992), 48, 2223-2311) has become by far the most widely used coupling chemistry for the synthesis of oligonucleotides. As is well known to those skilled in the art, phosphoramidite synthesis of oligonucleotides involves activation of nucleoside phosphoramidite monomer precursors by reaction with an activating agent to form activated intermediates, followed by sequential addition of the activated intermediates to the growing oligonucleotide chain (generally anchored at one end to a suitable solid support) to form the oligonucleotide product. Tetrazole is commonly used for the activation of the nucleoside phosphoramidite monomers; the activation occurs by the mechanism depicted in Scheme I. Tetrazole has an acidic proton which presumably protonates the basic nitrogen of the diisopropylamino phosphine group, thus making the diisopropylamino group a leaving group. The negatively charged tetrazolium ion then makes an attack on the trivalent phosphorous, forming a transient phosphorous tetrazolide species. The 5'-OH group of the solid support bound nucleoside then attacks the active trivalent phosphorous species, resulting in the formation of the internucleotide linkage.
The trivalent phosphorous is finally oxidized to the pentavalent phosphorous.
Scheme 1
1 ) Repetition of cycles
2) Cleave and deprotect with NH4OH or CH3NH2/NH4OH
Biologically active oligonucleotides
Principal drawbacks of tetrazole are its cost and instability which includes its potential to explode (Material Safety Data Sheets or MSDS lists IH-tetrazole as a severe explosion hazard). Because of its inherent instability, sublimed tetrazole is generally required to ensure desired coupling yields. Further, tetrazole (which is typically used near its saturated solubility of 0.5M) tends to precipitate out of acetonitrile solution at cold temperatures; this can lead to valve blockage on some automated DNA synthesizers. Other activators which work almost as efficiently as tetrazole have similar drawbacks to those of tetrazole as discussed above. These activators, which are all proton donors, include the following members of the tetrazole class of activators: 5-(p- nitrophenyl) tetrazole (Froehler, B. C. and Mattcucci, M. D., Tetrahedron Letters (1983), 24, 3171-3174); 5-(p-nitrophenyl) tetrazole and DMAP (Pon, R.T., Tetrahedron Letters (1987), 28, 3643-3646); and 5-(ethylthio)- IH-tetrazole (Wright, P. et al., Tetrahedron
Letters (1993), 34, 3373-3376). In addition to the tetrazole class of activators, the
following activators have been employed: N-methylaniline trifluoroacetate (Fourrey, J. L. and Varenne, J., Tetrahedron Letters (1984), 25, 4511-4514); N-methyl anilinium trichloroacetate (Fourrey, J. L. et al., Tetrahedron Letters (1987), 28, 1769-1772); 1-methylimidazoletrifluoromethane sulfonate (Arnold, L. et al., Collect. Czech. Chem. Commun. (1989), 54, 523-532); octanoic acid or triethylamine (Stec, W. J. and Zon, G.,
Tetrahedron Letters (1984), 25, 5279-5282); 1-methylimidazole HC1, 5-trifluoromethyl- lH-tetrazole, N,N-dimethylaniline HC1, and N,N-dimethylaminopyridine HC1 (Hering, G. et al., Nucleosides and Nucleotides (1985), 4, 169-171). Overall, these activators gave inferior performance relative to tetrazole. JP 08301878 discloses the use of another proton activator. A 1 :1 mixture of benzimidazole and BF3 etherate is disclosed wherein the BF3 component acts to increase the acidity of the benzimidazole proton necessary for activation of the phosphoramidite (intermediates). The benzimidazole BF3 complex acts in a manner similar to tetrazole described in Scheme 1. The present invention does not activate phosphoramidite intermediates with a proton donor but instead utilizes Lewis acids for activation. In particular, BF3 etherate is used in the present invention. The advantages of BF3 etherate over the benzimidazole BF3 complex include commercial availability and ease of removal of diethyl ether versus removal of benzimidazole.
Furthermore, the activated phosphoramidite intermediates are highly sensitive to moisture. An excess of 50% to 100% of the highly valuable phosphoramidites are required for sequencing even with anhydrous solvents (<20 ppm moisture content). The presence of trace amounts of moisture results in considerable loss of yield and an increase in deleted sequencing impurities. In addition to activating phosphoramidite intermediates, Lewis acids can act as moisture scavengers minimizing decomposition of the phosphoramidite. Therefore, the use of Lewis acids for activation of phosphoramidite intermediates leads to improved coupling efficiency, lower cost, and convenient material handling and operation.
Addition of a Lewis acid, however, can lower the pH of the reaction mixture. The increased acidity in the reaction mixture may cause the removal of N- and O-protecting groups on the phosphoramidite intermediate leading to undesirable products and reduced
yields. The addition of pyridine may therefore be used to increase the pH to a level that the phosphoramidite protecting groups can tolerate.
It is an object of the present invention to provide Lewis acid activated nucleosides for use in synthesis, including solid phase synthesis, which do not exhibit all of the drawbacks of the prior art.
It is a further object of the present invention to provide methods for the preparation and use of Lewis acid activated nucleosides as hereinafter described.
Summary of the Invention In its principle embodiment, the present invention discloses a process for activating phophoramidite monomers of formula I:
I, wherein B1 is selected from the group consisting of a purine base and a pyrimidine base; R1 is a secondary amine, a preferred amine is diisopropylamine;
R2 is selected from the group consisting of alkoxy, alkyl, alkylsulfonylalkoxy arylsulfonylalkoxy, cyanoalkoxy, and haloalkoxy;
R3 is a hydroxy-protecting group, a preferred group is 4-4'-dimethoxytrityl; and
R4 is selected from the group consisting of hydrogen and -OR7 wherein, R7 is a hydroxy- protecting group; comprising treating the phosphoramidite monomers of formula I with an optional amount of pyridine and a Lewis acid, preferred Lewis acids are selected from aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride and zirconium(IN) chloride.
Detailed Description of the Invention
All patents, patent applications, and literature references cited in the specification are hereby incorporated by reference in their entirety. In the case of inconsistencies, the present disclosure, including definitions, will prevail.
Definition of Terms
As used in the specification and the appended claims, the following terms have the meanings specified.
The term "alkoxy," as used herein, refers to an alkyl group, as defined herein, appended to the parent molecular moiety through an oxy group, as defined herein.
Representative examples of alkoxy include, but are not limited to, methoxy, ethoxy, propoxy, 2-propoxy, butoxy, tert-butoxy, pentyloxy, and the like.
The term "alkyl," as used herein, refers to a straight or branched chain hydrocarbon containing from 1 to 5 carbon atoms. Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec-butyl, iso-butyl, tert-butyl, n-pentyl, and the like.
The term "alkylcarbonyl," as used herein, refers to an alkyl group, as defined herein, appended to the parent molecular moiety through a carbonyl group, as defined herein. Representative examples of alkylcarbonyl include, but are not limited to, acetyl, ethylcarbonyl, and the like.
The term "alkylcarbonyloxy," as used herein, refers to an alkylcarbonyl group, as defined herein, appended to the parent molecular moiety through an oxy group, as defined herein. Representative examples of alkylcarbonyloxy include, but are not limited to, acetyloxy, ethylcarbonyloxy, t-butylcarbonyloxy, and the like. The term "alkylsulfonyl," as used herein, refers to an alkyl group, as defined herein, appended to the parent molecular moiety through a sulfonyl group, as defined herein. Representative examples of alkylsulfonyl include, but are not limited to, methylsulfonyl, ethylsulfonyl, and the like.
The term "alkylsulfonylalkoxy," as used herein, refers to an alkylsulfonyl group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as
defined herein. Representative examples of alkylsulfonylalkoxy include, but are not limited to, 2-methylsulfonylethoxy, 2-ethylsulfonylethoxy, and the like. The term "amino," as used herein, refers to a -NH2 group. The term "amino-protecting group" or "N-protecting group,"refers to groups intended to protect an amino group against undersirable reactions during synthetic procedures. Commonly used nitrogen-protecting groups are disclosed in Greene, T. W., &
Wuts, P. G. M. (1991). Protectective Groups In Organic Synthesis (2nd ed.). New York:
John Wiley & Sons. Preferred nitrogen-protecting groups are formyl, acetyl, benzoyl, pivaloyl, t-butylacetyl, phenylsulfonyl, benzyl, t-butyloxycarbonyl (Boc), and benzyloxycarbonyl (Cbz).
The term "aryl," as used herein, refers to an aromatic monocyclic ring system, or a bicyclic-fused ring system wherein one or both of the fused rings are aromatic.
Representative examples of aryl include, but are not limited to, azulene, indanyl, indenyl, naphthyl, phenyl, tetrahydronaphthyl, and the like. The aryl groups of this invention can be substituted with 1, 2, or 3 substituents independently selected from alkyl, cyano, halogen, haloalkyl, and nitro.
The term "arylalkoxy," as used herein, refers to an aryl group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein.
Representative examples of arylalkoxy include, but are not limited to, 2-phenylethoxy, 2-naphthylethoxy, 2-(4-nitrophenyl)ethoxy, and the like.
The term "arylsulfonyl," as used herein, refers to an aryl group, as defined herein, appended to the parent molecular moiety through a sulfonyl group, as defined herein.
Representative examples of arylsulfonyl include, but are not limited to, phenylsulfonyl, naphthylsulfonyl, and the like. The term "arylsulfonylalkoxy," as used herein, refers to an arylsulfonyl group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein. Representative examples of arylsulfonylalkoxy include, but are not limited to, 2-phenylsulfonylethoxy, 3-phenylsulfonylpropoxy, and the like. The term "carbonyl," as used herein, refers to a -C(O)- group. The term "catechol," as used herein, refers to a C6H4- 1 ,2-(O-)2 group, wherein both oxygen atoms are attached to M, as defined herein.
The term "cyano," as used herein, refers to a -CN group.
The term "cyanoalkoxy," as used herein, refers to a cyano group, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein. Representative examples of cyanoalkoxy include, but are not limited to, 2-cyanoethoxy, 3-cyanopropoxy, 1 -methyl-2-cyanoethoxy, l,l-dimethyl-2-cyanoethoxy, and the like.
The term "halo" or "halogen," as used herein, refers to -Cl, -Br, -I or -F. The term "haloalkoxy," as used herein, refers to at least one halogen, as defined herein, appended to the parent molecular moiety through an alkoxy group, as defined herein. Representative examples of haloalkoxy include, but are not limited to, 2,2,2- trichloroethoxy, l,l-dimethyl-2,2,2-trichloroethoxy, trifluoromethoxy, and the like.
The term "haloalkyl," as used herein, refers to at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2- fluoroethyl, trifiuoromethyl, pentafluoroethyl, 2-chloro-3-fluoropentyl, and the like.
The term "hydroxy-protecting group" or "O-protecting group" refers to groups intended to protect a hydroxy group against undesirable reactions during synthetic procedures. Commonly used hydroxy-protecting groups are disclosed in T.H. Greene and P.G.M. Wuts, Protective Groups in Organic Synthesis. 2nd edition, John Wiley & Sons, New York (1991), which is hereby incorporated by reference. Examples of hydroxy- protecting groups include, but are not limited to, substituted methyl ethers, for example, methoxymethyl, benzyloxymethyl, 2-methoxyethoxymethyl, 2-(trimethylsilyl)- ethoxymethyl, benzyl, and triphenylmethyl; tetrahydropyranyl ethers; substituted ethyl ethers, for example, 2,2,2-trichloroethyl and t-butyl; silyl ethers, for example, trimethylsilyl, t-butyldimethylsilyl and t-butyldiphenylsilyl; cyclic acetals and ketals, for example, methylene acetal, acetonide and benzylidene acetal; cyclic ortho esters, for example, methoxymethylene; cyclic carbonates; cyclic boronates; carbonyl derivatives, for example, acetyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,4- dinitrophenylethoxylcarbonyl, 2-(methylthiomethoxymethyl)benzoyl, 2- (isopropylthiomethoxymethyl)benzoyl, 2-(2,4- dinitrobenzenesulphenyloxymethyl)benzoyl, 4-(methylthiomethoxy)butyryl, and levulinyl;
trityl derivatives, for example, 4,4'-dimethoxytrityl, 4,4',4"-tris-(benzyloxy)trityl, 4,4',4"- tris-(4,5-dichlorophthalimido)trityl, 4,4',4"-tris-(levulinyloxy)trityl, 3-(imidazolylmethyl)- 4,4'-dimethoxytrityl, 4-decyloxytrityl, 4-hexadecyloxytrityl and l,l-bis-(4-methoxyhenyl)- l'-pyrenylmethyl; substituted xanthenyl groups, for example, pixyl(9-phenylxanthen-9-yl), 9-(p-methoxyphenyl)xanthen-9-yl), and 9-(4-octadecyloxyphenyl)xanthene-9-yl.
The term "Lewis acid," as used herein, refers to a chemical species, other than a proton, that has a vacant orbital or accepts an electron pair. It is to be understood that Lewis acids can be purchased or prepared as complexes including but not limited to, etherates, hydrates, and thioetherates. It is to be further understood that complexes purchased or prepared for the present invention do not contain an acidic proton.
Representative examples of Lewis acid include, but are not limited to, aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride, zirconium(IV) chloride, and the like. The term "methylenedioxy," as used herein, refers to a -OC(R80)(R81)O- group wherein R80 and R81 are independently selected from hydrogen and alkyl. The oxygen atoms of the methylenedioxy group are attached to the parent molecular moiety through two adjacent carbon atoms. Representative examples of a methylenedioxy group include, but are not limited to, 1,3-dioxolanyl, 2,2-dimethyl-l,3-dioxolanyl, 2-methyl-l,3- dioxolanyl, and the like.
The term "oxy," as used herein, refers to (-O-).
The term "purine base," as used herein, refers to an organic base selected from 9H-purin-6-ylamine (adenine) and 2-amino-l,9-dihydro-6H-purin-6-one (guanine). The amino group attached to adenine can be protected with a nitrogen-protecting group. The term "proton," as used herein, refers to H+.
The term "pyrimidine base," as used herein, refers to an organic base selected from 2,4(lH,3H)-pyrimidinedione (uracil), 5-methyl-2,4(lH,3H)-pyrimidinedione (thymine), and 4-amino-2(lH)-pyrimidinone (cytosine). The amino group attached to cytosine can be protected with a nitrogen-protecting group. The term "sulfonyl," as used herein, refers to a -SO2- group.
The term "trifluoromethane," as used herein, refers to a -CF3 group.
The term "trifluoromethanesulfonyl," as used herein, refers to a trifluoromethane group, as defined herein, appended to the parent molecular moiety through a sulfonyl group, as defined herein.
The term "trifluoromethanesulfonyloxy," as used herein, refers to a trifluoromethanesulfonyl group, as defined herein, appended to the parent molecular moiety through an oxy group, as defined herein.
Abbreviations
The following abbreviations are used: DMA for dimethylacetamide, DMT for 4,4'- dimethoxytrityl, EtOAc for ethyl acetate, eq for equivalents, MSDS for Material Safety
Data Sheets, NaHCO3 for sodium bicarbonate, Na2SO4 for sodium sulfate, and TLC for thin layer chromatography.
Synthetic Methods The compounds and processes of the present invention will be better understood in connection with the following synthetic scheme which illustrates the method by which the compounds of the invention may be prepared.
Scheme 1
π -2 equivalents Lewis acid 0-2 equivalents
pyridine
(i) (ϋ)
(iii)
General procedure using Lewis acids as activators:
A solution of phosphoramidite (i) (1.0 eq) and nucleoside (ii) (1.0 eq) in acetonitrile or DMA (0.1 M) was treated with a Lewis acid (Table 1). The solution was mixed at room temperature and was monitored by TLC using EtOAc :triethylamine (95:5) as the developing solvent. After a range of less than 5 minutes to 60 minutes (Table 1), the reaction mixture was quenched with aqueous NaHCO3 and extracted with EtOAc. The organic layer was washed with aqueous NaHCO3, dried (Na2SO4), and evaporated under vacuum to provide the dimer product (iii) in approximately quantitative yield. 3,P NMR (500 MHz, CD2C12) δ 139.5, 139.7;
MS (ESr) m/z: 1041.4 (M+).
General procedure using Lewis acids and pyridine as activators: A solution of phosphoramidite (i) (1.0 eq) and nucleoside (ii) (1.0 eq) in acetonitrile or DMA (0.1 M) was treated with pyridine (2 eq) followed by the addition of a Lewis acid (2 eq). The solution was mixed at room temperature and was monitored by TLC using EtOAc :triethylamine (95:5) as the developing solvent. After less than 5 minutes, the reaction mixture was quenched with aqueous NaHCO3 and extracted with EtOAc. The organic layer was washed with aqueous NaHCO3, dried (Na2SO4), and evaporated under vacuum to provide the dimer product (iii) in approximately quantitative yield.
31P NMR (500 MHz, CD2C12) δ 139.5, 139.7; MS (ESL) m/z: 1041.4 (M+).
Table 1
It is to be understood that dimer (iii) can be oxidizied using standard conditions know to those of ordinary skill in the art to give the phosphate, (J. Am. Chem. Soc,
(1976), 98, 3655-3661). The 5'-OH of the oxidized dimer can be deprotected and treated with a Lewis acid activated phophoramidite monomer to form a trimer. This sequence of steps can be repeated until an oligonucleotide of desired length has been synthesized such that the process of the present invention can be used for preparing oligonucleotides, including solid phase synthesis thereof.
Claims
WE CLAIM:
1. A composition comprising a Lewis acid, an optional amount of pyridine, and a compound of formula I:
R2^P Rι I, wherein,
B1 is selected from the group consisting of a purine base and a pyrimidine base; R1 is -NR5R6, wherein, R5 and R6 are independently selected from the group consisting of alkyl and arylalkyl; R2 is selected from the group consisting of alkoxy, alkyl, alkylsulfonylalkoxy arylsulfonylalkoxy, cyanoalkoxy, and haloalkoxy; R3 is a hydroxy-protecting group;
R4 is selected from the group consisting of hydrogen and -OR7, wherein R7 is a hydroxy-protecting group.
A composition according to claim 1 comprising said Lewis acid of formula II:
π, wherein, M is selected from the group consisting of aluminum, antimony, bismuth, boron, cadmium, cobalt, copper, chromium, gold, hafnium, iridium, iron, lanthanum, magnesium, manganese, mercury, molybdenum, nickel, niobium, osmium, palladium, platinum, phosphorous, rhenium, ruthenium, scandium, silver, tantalum, tellurium, tin, tungsten, titanium, vanadium, zinc, zirconium, and yttrium; R10 is selected from the group consisting of alkoxy, alkylcarbonyloxy, trifluoromethanesulfonyloxy, cyano, and halogen; R" is absent or selected from the group consisting of alkoxy, alkylcarbonyloxy,
trifluoromethanesulfonyloxy, cyano, and halogen; or R10 and R11 taken together form a catechol wherein both oxygen atoms are attached to M;
R12 is absent or selected from the group consisting of alkoxy, alkylcarbonyloxy, trifluoromethanesulfonyloxy, cyano, and halogen;
R13 is absent or selected from the group consisting of alkoxy, alkylcarbonyloxy, trifluoromethanesulfonyloxy, cyano, and halogen; and
R14 is absent or selected from the group consisting of halogen.
3. A composition according to claim 2 comprising said Lewis acid of formula II wherein,
M is selected from the group consisting of aluminum, bismuth, boron, iron, magnesium, manganese, titanium, zinc, and zirconium;
R10 is selected from the group consisting of alkoxy, cyano, halogen and trifluoromethanesulfonyloxy;
RH is selected from the group consisting of alkoxy, cyano, halogen and trifluoromethanesulfonyloxy; or
R10 and R" taken together form a catechol wherein both oxygen atoms are attached to M;
R12 is absent or selected from the group consisting of alkoxy and halogen;
R13 is absent or selected from the group consisting of alkoxy and halogen; and
R14 is absent. 4. A composition according to claiml comprising, said Lewis acid selected from the group consisting of aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride and zirconium(IV) chloride.
5. A composition according to claiml , wherein R5 and R6 are independently selected from the group consisting of alkyl.
6. A composition according to claim 1, wherein R5 is isopropyl; and
R6 is isopropyl.
7. A composition according to claim 1, wherein R2 is selected from the group consisting of cyanoalkoxy.
8. A composition according to claim 1, wherein R2 is 2-cyanoethoxy.
9. A composition according to claim 1, wherein R1 is diisopropylamino; and R2 is 2-cyanoethoxy.
10. A composition according to claim 1, wherein R3 is selected from the group consisting of 4,4'-dimethoxytrityl, 4,4',4"-tris-(benzyloxy)trityl, 4,4',4"-tris-(4,5- dichlorophthalimido)trityl, 4,4',4"-tris-(levulinyloxy)trityl, 3-(imidazolylmethyl)- 4,4',-dimethoxytrityl, pixyl(9-phenylxanthen-9-yl), 9-(p- methoxyphenyl)xanthen-9-yl), 4-decyloxytrityl, 4-hexadecyloxytrityl, 9-(4- octadecyloxyphenyl)xanthene-9-yl, 1 , 1 -bis-(4-methoxyhenyl)-l'-pyrenylmethyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,4- dinitrophenylethoxylcarbonyl, 4-(methylthiomethoxy)butyryl, 2- (methylthiomethoxymethyl)benzoyl, 2-(isopropylthiomethoxymethyl)benzoyl, 2-
(2,4-dinitrobenzenesulphenyloxymethyl)benzoyl, and levulinyl.
11. A composition according to claim 1, wherein R3 is 4,4'-dimethoxytrityl.
12. A composition according to claim 1 comprising 1-4 molar equivalents of pyridine.
3. A composition according to claim 1 comprising, said Lewis acid selected from the group consisting of aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride and zirconium(IV) chloride;
0-4 molar equivalents of pyridine; and said compound of formula I wherein,
R1 is diisopropylamino;
R2 is 2-cyanoethoxy; and R3 is 4,4'-dimethoxytrityl.
14. A process for the preparation of a compound of formula III:
III, wherein B1 and B2 are independently selected from the group consisting of a purine base and a pyrimidine base;
R2 is selected from the group consisting of alkoxy, alkyl, alkylsulfonylalkoxy arylsulfonylalkoxy, cyanoalkoxy, and haloalkoxy;
R3 is a hydroxy-protecting group; R4 is selected from the group consisting of hydrogen and -OR7;
R8 is -OR7; and
R9 is selected from the group consisting of hydrogen and -OR7; or
R8 and R9 taken together form a methylenedioxy group;
said process comprising treating a composition according to claim 1 with a compound of formula IV,
IV.
15. A process according to claim 14, wherein R2 is alkyl.
16. A process according to claim 14, wherein R2 is cyanoalkoxy.
17. A process according to claim 14, wherein
R2 is 2-cyanoethoxy; and R8 and R9 taken together form a methylenedioxy group.
18. A process according to claim 14, wherein R2 is 2-cyanoethoxy;
R3 is 4,4'-dimethoxytrityl;
R4 is hydrogen;
R8 and R9 taken together form a methylenedioxy group.
19. A process of oligonucleotide synthesis in which nucleoside phosphoramidite monomer precursors are activated by treatment with a Lewis acid to form activated intermediates and the activated intermediates are sequentially added to form an oligonucleotide product, wherein the improvement comprises using said Lewis acid as a phosphoramidite monomer activator.
0. A process according to claim 19 wherein, said Lewis acid is selected from the group consisting of aluminum chloride, bismuth(III) chloride, boron trifluoride, iron(II) chloride, iron(III) chloride, magnesium bromide, magnesium chloride, magnesium trifluoromethanesulfonate, manganese(II) chloride, zinc bromide, zinc chloride and zirconium(IV) chloride.
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| PCT/US2000/012530 WO2000075157A1 (en) | 1999-06-03 | 2000-05-08 | Oligonucleotide synthesis with lewis acids as activators |
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| CA3172483A1 (en) | 2020-04-06 | 2021-10-14 | Scott Ellis | Inhalation formulations of 1'-cyano substituted carbanucleoside analogs |
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| JPH08301878A (en) * | 1995-04-28 | 1996-11-19 | Toagosei Co Ltd | Synthesis of boron trifluoride coordinated compound and oligonucleotide |
-
2000
- 2000-05-08 JP JP2001502438A patent/JP2003514766A/en not_active Withdrawn
- 2000-05-08 MX MXPA01012444A patent/MXPA01012444A/en unknown
- 2000-05-08 CA CA002376016A patent/CA2376016A1/en not_active Abandoned
- 2000-05-08 WO PCT/US2000/012530 patent/WO2000075157A1/en not_active Ceased
- 2000-05-08 EP EP00926516A patent/EP1181301A1/en not_active Withdrawn
Non-Patent Citations (1)
| Title |
|---|
| See references of WO0075157A1 * |
Also Published As
| Publication number | Publication date |
|---|---|
| MXPA01012444A (en) | 2002-07-30 |
| JP2003514766A (en) | 2003-04-22 |
| CA2376016A1 (en) | 2000-12-14 |
| WO2000075157A1 (en) | 2000-12-14 |
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