WO1994012518A2 - Reactif pour le couplage de diverses substances a des acides nucleiques et procede pour sa preparation - Google Patents
Reactif pour le couplage de diverses substances a des acides nucleiques et procede pour sa preparation Download PDFInfo
- Publication number
- WO1994012518A2 WO1994012518A2 PCT/DE1993/001101 DE9301101W WO9412518A2 WO 1994012518 A2 WO1994012518 A2 WO 1994012518A2 DE 9301101 W DE9301101 W DE 9301101W WO 9412518 A2 WO9412518 A2 WO 9412518A2
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- ribooligonucleotide
- rna
- reagent
- nucleic acids
- molecule
- Prior art date
Links
- 238000005859 coupling reaction Methods 0.000 title claims abstract description 61
- 230000008878 coupling Effects 0.000 title claims abstract description 60
- 238000010168 coupling process Methods 0.000 title claims abstract description 60
- 150000007523 nucleic acids Chemical class 0.000 title claims abstract description 38
- 108020004707 nucleic acids Proteins 0.000 title claims abstract description 37
- 102000039446 nucleic acids Human genes 0.000 title claims abstract description 37
- 238000000034 method Methods 0.000 title claims abstract description 28
- 239000003153 chemical reaction reagent Substances 0.000 title claims description 65
- 239000000126 substance Substances 0.000 title claims description 19
- 239000003550 marker Substances 0.000 claims abstract description 21
- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 claims abstract description 18
- 101710086015 RNA ligase Proteins 0.000 claims abstract description 15
- 102000004169 proteins and genes Human genes 0.000 claims abstract description 11
- 108090000623 proteins and genes Proteins 0.000 claims abstract description 11
- 239000002777 nucleoside Chemical group 0.000 claims abstract description 9
- 125000004435 hydrogen atom Chemical group [H]* 0.000 claims abstract description 8
- 239000002773 nucleotide Substances 0.000 claims abstract description 7
- 101710163270 Nuclease Proteins 0.000 claims abstract description 6
- 150000003833 nucleoside derivatives Chemical group 0.000 claims abstract description 6
- 125000002887 hydroxy group Chemical group [H]O* 0.000 claims abstract description 5
- 230000008569 process Effects 0.000 claims abstract description 5
- 238000009396 hybridization Methods 0.000 claims abstract description 3
- 230000003993 interaction Effects 0.000 claims abstract description 3
- 229920002477 rna polymer Polymers 0.000 claims description 25
- 102000004190 Enzymes Human genes 0.000 claims description 16
- 108090000790 Enzymes Proteins 0.000 claims description 16
- 125000003277 amino group Chemical group 0.000 claims description 13
- 230000015572 biosynthetic process Effects 0.000 claims description 11
- 238000003786 synthesis reaction Methods 0.000 claims description 11
- GNBHRKFJIUUOQI-UHFFFAOYSA-N fluorescein Chemical class O1C(=O)C2=CC=CC=C2C21C1=CC=C(O)C=C1OC1=CC(O)=CC=C21 GNBHRKFJIUUOQI-UHFFFAOYSA-N 0.000 claims description 10
- SHIBSTMRCDJXLN-KCZCNTNESA-N digoxigenin Chemical class C1([C@@H]2[C@@]3([C@@](CC2)(O)[C@H]2[C@@H]([C@@]4(C)CC[C@H](O)C[C@H]4CC2)C[C@H]3O)C)=CC(=O)OC1 SHIBSTMRCDJXLN-KCZCNTNESA-N 0.000 claims description 7
- 230000026731 phosphorylation Effects 0.000 claims description 7
- 238000006366 phosphorylation reaction Methods 0.000 claims description 7
- 125000006850 spacer group Chemical group 0.000 claims description 7
- 108091034117 Oligonucleotide Proteins 0.000 claims description 6
- ISAKRJDGNUQOIC-UHFFFAOYSA-N Uracil Chemical compound O=C1C=CNC(=O)N1 ISAKRJDGNUQOIC-UHFFFAOYSA-N 0.000 claims description 6
- 238000005576 amination reaction Methods 0.000 claims description 6
- UHDGCWIWMRVCDJ-UHFFFAOYSA-N 1-beta-D-Xylofuranosyl-NH-Cytosine Natural products O=C1N=C(N)C=CN1C1C(O)C(O)C(CO)O1 UHDGCWIWMRVCDJ-UHFFFAOYSA-N 0.000 claims description 5
- UHDGCWIWMRVCDJ-PSQAKQOGSA-N Cytidine Natural products O=C1N=C(N)C=CN1[C@@H]1[C@@H](O)[C@@H](O)[C@H](CO)O1 UHDGCWIWMRVCDJ-PSQAKQOGSA-N 0.000 claims description 5
- UHDGCWIWMRVCDJ-ZAKLUEHWSA-N cytidine Chemical compound O=C1N=C(N)C=CN1[C@H]1[C@H](O)[C@@H](O)[C@H](CO)O1 UHDGCWIWMRVCDJ-ZAKLUEHWSA-N 0.000 claims description 5
- 125000000217 alkyl group Chemical group 0.000 claims description 4
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 claims description 4
- 238000004519 manufacturing process Methods 0.000 claims description 4
- 239000000523 sample Substances 0.000 claims description 4
- GFFGJBXGBJISGV-UHFFFAOYSA-N Adenine Chemical compound NC1=NC=NC2=C1N=CN2 GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 claims description 3
- 229930024421 Adenine Natural products 0.000 claims description 3
- 229960000643 adenine Drugs 0.000 claims description 3
- 238000007901 in situ hybridization Methods 0.000 claims description 3
- 229940035893 uracil Drugs 0.000 claims description 3
- 125000004057 biotinyl group Chemical class [H]N1C(=O)N([H])[C@]2([H])[C@@]([H])(SC([H])([H])[C@]12[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C(*)=O 0.000 claims 3
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- 239000003054 catalyst Substances 0.000 abstract 1
- 150000001875 compounds Chemical class 0.000 abstract 1
- 238000011835 investigation Methods 0.000 abstract 1
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 15
- 238000002372 labelling Methods 0.000 description 10
- 108020004414 DNA Proteins 0.000 description 9
- 238000006243 chemical reaction Methods 0.000 description 7
- 238000011534 incubation Methods 0.000 description 7
- -1 sulfonic acid chlorides Chemical class 0.000 description 7
- VKIGAWAEXPTIOL-UHFFFAOYSA-N 2-hydroxyhexanenitrile Chemical compound CCCCC(O)C#N VKIGAWAEXPTIOL-UHFFFAOYSA-N 0.000 description 6
- 235000018102 proteins Nutrition 0.000 description 6
- 238000007068 beta-elimination reaction Methods 0.000 description 5
- 239000003431 cross linking reagent Substances 0.000 description 5
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 5
- TWRXJAOTZQYOKJ-UHFFFAOYSA-L Magnesium chloride Chemical compound [Mg+2].[Cl-].[Cl-] TWRXJAOTZQYOKJ-UHFFFAOYSA-L 0.000 description 4
- 108091028043 Nucleic acid sequence Proteins 0.000 description 4
- ISWSIDIOOBJBQZ-UHFFFAOYSA-N Phenol Chemical compound OC1=CC=CC=C1 ISWSIDIOOBJBQZ-UHFFFAOYSA-N 0.000 description 4
- 125000003172 aldehyde group Chemical group 0.000 description 4
- 150000001615 biotins Chemical class 0.000 description 4
- 125000003835 nucleoside group Chemical group 0.000 description 4
- 125000003729 nucleotide group Chemical class 0.000 description 4
- KHIWWQKSHDUIBK-UHFFFAOYSA-N periodic acid Chemical compound OI(=O)(=O)=O KHIWWQKSHDUIBK-UHFFFAOYSA-N 0.000 description 4
- 150000008300 phosphoramidites Chemical class 0.000 description 4
- 125000006239 protecting group Chemical group 0.000 description 4
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- SHIBSTMRCDJXLN-UHFFFAOYSA-N Digoxigenin Natural products C1CC(C2C(C3(C)CCC(O)CC3CC2)CC2O)(O)C2(C)C1C1=CC(=O)OC1 SHIBSTMRCDJXLN-UHFFFAOYSA-N 0.000 description 3
- LYCAIKOWRPUZTN-UHFFFAOYSA-N Ethylene glycol Chemical compound OCCO LYCAIKOWRPUZTN-UHFFFAOYSA-N 0.000 description 3
- ZMXDDKWLCZADIW-UHFFFAOYSA-N N,N-Dimethylformamide Chemical compound CN(C)C=O ZMXDDKWLCZADIW-UHFFFAOYSA-N 0.000 description 3
- 230000006819 RNA synthesis Effects 0.000 description 3
- 108091028664 Ribonucleotide Proteins 0.000 description 3
- QONQRTHLHBTMGP-UHFFFAOYSA-N digitoxigenin Natural products CC12CCC(C3(CCC(O)CC3CC3)C)C3C11OC1CC2C1=CC(=O)OC1 QONQRTHLHBTMGP-UHFFFAOYSA-N 0.000 description 3
- KZNICNPSHKQLFF-UHFFFAOYSA-N dihydromaleimide Natural products O=C1CCC(=O)N1 KZNICNPSHKQLFF-UHFFFAOYSA-N 0.000 description 3
- 238000006911 enzymatic reaction Methods 0.000 description 3
- 125000005842 heteroatom Chemical group 0.000 description 3
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- 238000007254 oxidation reaction Methods 0.000 description 3
- 239000002336 ribonucleotide Substances 0.000 description 3
- 125000002652 ribonucleotide group Chemical group 0.000 description 3
- 229960002317 succinimide Drugs 0.000 description 3
- 229910052717 sulfur Inorganic materials 0.000 description 3
- PGZIDERTDJHJFY-UHFFFAOYSA-N 4-fluoro-7-nitro-2,1,3-benzoxadiazole Chemical compound [O-][N+](=O)C1=CC=C(F)C2=NON=C12 PGZIDERTDJHJFY-UHFFFAOYSA-N 0.000 description 2
- USFZMSVCRYTOJT-UHFFFAOYSA-N Ammonium acetate Chemical compound N.CC(O)=O USFZMSVCRYTOJT-UHFFFAOYSA-N 0.000 description 2
- 239000005695 Ammonium acetate Substances 0.000 description 2
- HMFHBZSHGGEWLO-SOOFDHNKSA-N D-ribofuranose Chemical compound OC[C@H]1OC(O)[C@H](O)[C@@H]1O HMFHBZSHGGEWLO-SOOFDHNKSA-N 0.000 description 2
- 230000006820 DNA synthesis Effects 0.000 description 2
- IAZDPXIOMUYVGZ-UHFFFAOYSA-N Dimethylsulphoxide Chemical compound CS(C)=O IAZDPXIOMUYVGZ-UHFFFAOYSA-N 0.000 description 2
- 229910019142 PO4 Inorganic materials 0.000 description 2
- PYMYPHUHKUWMLA-LMVFSUKVSA-N Ribose Natural products OC[C@@H](O)[C@@H](O)[C@@H](O)C=O PYMYPHUHKUWMLA-LMVFSUKVSA-N 0.000 description 2
- 229920005654 Sephadex Polymers 0.000 description 2
- 239000012507 Sephadex™ Substances 0.000 description 2
- 238000012300 Sequence Analysis Methods 0.000 description 2
- UIIMBOGNXHQVGW-UHFFFAOYSA-M Sodium bicarbonate Chemical compound [Na+].OC([O-])=O UIIMBOGNXHQVGW-UHFFFAOYSA-M 0.000 description 2
- WYURNTSHIVDZCO-UHFFFAOYSA-N Tetrahydrofuran Chemical compound C1CCOC1 WYURNTSHIVDZCO-UHFFFAOYSA-N 0.000 description 2
- IQFYYKKMVGJFEH-XLPZGREQSA-N Thymidine Chemical compound O=C1NC(=O)C(C)=CN1[C@@H]1O[C@H](CO)[C@@H](O)C1 IQFYYKKMVGJFEH-XLPZGREQSA-N 0.000 description 2
- 239000002253 acid Substances 0.000 description 2
- OIRDTQYFTABQOQ-KQYNXXCUSA-N adenosine group Chemical group [C@@H]1([C@H](O)[C@H](O)[C@@H](CO)O1)N1C=NC=2C(N)=NC=NC12 OIRDTQYFTABQOQ-KQYNXXCUSA-N 0.000 description 2
- HMFHBZSHGGEWLO-UHFFFAOYSA-N alpha-D-Furanose-Ribose Natural products OCC1OC(O)C(O)C1O HMFHBZSHGGEWLO-UHFFFAOYSA-N 0.000 description 2
- 229940043376 ammonium acetate Drugs 0.000 description 2
- 235000019257 ammonium acetate Nutrition 0.000 description 2
- 239000002585 base Substances 0.000 description 2
- 230000008901 benefit Effects 0.000 description 2
- 125000005340 bisphosphate group Chemical group 0.000 description 2
- 239000000872 buffer Substances 0.000 description 2
- 125000004432 carbon atom Chemical group C* 0.000 description 2
- 238000004132 cross linking Methods 0.000 description 2
- 150000002540 isothiocyanates Chemical class 0.000 description 2
- 229910001629 magnesium chloride Inorganic materials 0.000 description 2
- 239000003607 modifier Substances 0.000 description 2
- 229940046166 oligodeoxynucleotide Drugs 0.000 description 2
- NBIIXXVUZAFLBC-UHFFFAOYSA-K phosphate Chemical compound [O-]P([O-])([O-])=O NBIIXXVUZAFLBC-UHFFFAOYSA-K 0.000 description 2
- 239000010452 phosphate Substances 0.000 description 2
- 125000002924 primary amino group Chemical group [H]N([H])* 0.000 description 2
- 238000000163 radioactive labelling Methods 0.000 description 2
- 238000007086 side reaction Methods 0.000 description 2
- JQWHASGSAFIOCM-UHFFFAOYSA-M sodium periodate Chemical compound [Na+].[O-]I(=O)(=O)=O JQWHASGSAFIOCM-UHFFFAOYSA-M 0.000 description 2
- 125000001424 substituent group Chemical group 0.000 description 2
- JWDFQMWEFLOOED-UHFFFAOYSA-N (2,5-dioxopyrrolidin-1-yl) 3-(pyridin-2-yldisulfanyl)propanoate Chemical compound O=C1CCC(=O)N1OC(=O)CCSSC1=CC=CC=N1 JWDFQMWEFLOOED-UHFFFAOYSA-N 0.000 description 1
- JKMHFZQWWAIEOD-UHFFFAOYSA-N 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid Chemical compound OCC[NH+]1CCN(CCS([O-])(=O)=O)CC1 JKMHFZQWWAIEOD-UHFFFAOYSA-N 0.000 description 1
- NERWJJDOEYIOPM-UHFFFAOYSA-N 3-[[di(propan-2-yl)amino]-ethyl-dihydroxy-lambda5-phosphanyl]propanenitrile Chemical compound CC(C)N(C(C)C)P(O)(O)(CC)CCC#N NERWJJDOEYIOPM-UHFFFAOYSA-N 0.000 description 1
- BZTDTCNHAFUJOG-UHFFFAOYSA-N 6-carboxyfluorescein Chemical compound C12=CC=C(O)C=C2OC2=CC(O)=CC=C2C11OC(=O)C2=CC=C(C(=O)O)C=C21 BZTDTCNHAFUJOG-UHFFFAOYSA-N 0.000 description 1
- DWRXFEITVBNRMK-UHFFFAOYSA-N Beta-D-1-Arabinofuranosylthymine Natural products O=C1NC(=O)C(C)=CN1C1C(O)C(O)C(CO)O1 DWRXFEITVBNRMK-UHFFFAOYSA-N 0.000 description 1
- 108091003079 Bovine Serum Albumin Proteins 0.000 description 1
- 238000001712 DNA sequencing Methods 0.000 description 1
- KDXKERNSBIXSRK-UHFFFAOYSA-N Lysine Natural products NCCCCC(N)C(O)=O KDXKERNSBIXSRK-UHFFFAOYSA-N 0.000 description 1
- 239000004472 Lysine Substances 0.000 description 1
- NQTADLQHYWFPDB-UHFFFAOYSA-N N-Hydroxysuccinimide Chemical class ON1C(=O)CCC1=O NQTADLQHYWFPDB-UHFFFAOYSA-N 0.000 description 1
- 108010021757 Polynucleotide 5'-Hydroxyl-Kinase Proteins 0.000 description 1
- 102000008422 Polynucleotide 5'-hydroxyl-kinase Human genes 0.000 description 1
- 238000003559 RNA-seq method Methods 0.000 description 1
- 239000002262 Schiff base Substances 0.000 description 1
- 150000004753 Schiff bases Chemical class 0.000 description 1
- VMHLLURERBWHNL-UHFFFAOYSA-M Sodium acetate Chemical compound [Na+].CC([O-])=O VMHLLURERBWHNL-UHFFFAOYSA-M 0.000 description 1
- NINIDFKCEFEMDL-UHFFFAOYSA-N Sulfur Chemical compound [S] NINIDFKCEFEMDL-UHFFFAOYSA-N 0.000 description 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 Chemical class 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 1
- 238000010521 absorption reaction Methods 0.000 description 1
- 150000007513 acids Chemical class 0.000 description 1
- 230000003321 amplification Effects 0.000 description 1
- 150000001540 azides Chemical class 0.000 description 1
- IQFYYKKMVGJFEH-UHFFFAOYSA-N beta-L-thymidine Natural products O=C1NC(=O)C(C)=CN1C1OC(CO)C(O)C1 IQFYYKKMVGJFEH-UHFFFAOYSA-N 0.000 description 1
- 229940098773 bovine serum albumin Drugs 0.000 description 1
- 229910052799 carbon Inorganic materials 0.000 description 1
- 238000006555 catalytic reaction Methods 0.000 description 1
- 239000003795 chemical substances by application Substances 0.000 description 1
- 238000004140 cleaning Methods 0.000 description 1
- 238000003776 cleavage reaction Methods 0.000 description 1
- 125000000151 cysteine group Chemical group N[C@@H](CS)C(=O)* 0.000 description 1
- 239000005547 deoxyribonucleotide Substances 0.000 description 1
- 125000002637 deoxyribonucleotide group Chemical group 0.000 description 1
- 230000001419 dependent effect Effects 0.000 description 1
- VHJLVAABSRFDPM-QWWZWVQMSA-N dithiothreitol Chemical compound SC[C@@H](O)[C@H](O)CS VHJLVAABSRFDPM-QWWZWVQMSA-N 0.000 description 1
- 230000002255 enzymatic effect Effects 0.000 description 1
- 125000006125 ethylsulfonyl group Chemical group 0.000 description 1
- 238000000605 extraction Methods 0.000 description 1
- 239000007850 fluorescent dye Substances 0.000 description 1
- 238000001215 fluorescent labelling Methods 0.000 description 1
- 239000011521 glass Substances 0.000 description 1
- 229940042795 hydrazides for tuberculosis treatment Drugs 0.000 description 1
- 238000005342 ion exchange Methods 0.000 description 1
- 238000004255 ion exchange chromatography Methods 0.000 description 1
- 239000012948 isocyanate Substances 0.000 description 1
- 150000002513 isocyanates Chemical class 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 238000003199 nucleic acid amplification method Methods 0.000 description 1
- 238000002515 oligonucleotide synthesis Methods 0.000 description 1
- 239000003960 organic solvent Substances 0.000 description 1
- 230000001590 oxidative effect Effects 0.000 description 1
- 125000004430 oxygen atom Chemical group O* 0.000 description 1
- 125000000636 p-nitrophenyl group Chemical group [H]C1=C([H])C(=C([H])C([H])=C1*)[N+]([O-])=O 0.000 description 1
- 239000011148 porous material Substances 0.000 description 1
- 238000001556 precipitation Methods 0.000 description 1
- 150000003141 primary amines Chemical class 0.000 description 1
- 238000000746 purification Methods 0.000 description 1
- 150000003254 radicals Chemical class 0.000 description 1
- 239000002901 radioactive waste Substances 0.000 description 1
- 230000035484 reaction time Effects 0.000 description 1
- PYWVYCXTNDRMGF-UHFFFAOYSA-N rhodamine B Chemical compound [Cl-].C=12C=CC(=[N+](CC)CC)C=C2OC2=CC(N(CC)CC)=CC=C2C=1C1=CC=CC=C1C(O)=O PYWVYCXTNDRMGF-UHFFFAOYSA-N 0.000 description 1
- 239000002342 ribonucleoside Substances 0.000 description 1
- 150000008223 ribosides Chemical group 0.000 description 1
- 230000007017 scission Effects 0.000 description 1
- 125000003808 silyl group Chemical group [H][Si]([H])([H])[*] 0.000 description 1
- 239000001632 sodium acetate Substances 0.000 description 1
- 235000017281 sodium acetate Nutrition 0.000 description 1
- 229910000030 sodium bicarbonate Inorganic materials 0.000 description 1
- 235000017557 sodium bicarbonate Nutrition 0.000 description 1
- 239000007790 solid phase Substances 0.000 description 1
- 238000002798 spectrophotometry method Methods 0.000 description 1
- 238000003860 storage Methods 0.000 description 1
- 239000000758 substrate Substances 0.000 description 1
- 150000003463 sulfur Chemical class 0.000 description 1
- 239000011593 sulfur Substances 0.000 description 1
- 125000004434 sulfur atom Chemical group 0.000 description 1
- QSUJAUYJBJRLKV-UHFFFAOYSA-M tetraethylazanium;fluoride Chemical compound [F-].CC[N+](CC)(CC)CC QSUJAUYJBJRLKV-UHFFFAOYSA-M 0.000 description 1
- YLQBMQCUIZJEEH-UHFFFAOYSA-N tetrahydrofuran Natural products C=1C=COC=1 YLQBMQCUIZJEEH-UHFFFAOYSA-N 0.000 description 1
- WGTODYJZXSJIAG-UHFFFAOYSA-N tetramethylrhodamine chloride Chemical compound [Cl-].C=12C=CC(N(C)C)=CC2=[O+]C2=CC(N(C)C)=CC=C2C=1C1=CC=CC=C1C(O)=O WGTODYJZXSJIAG-UHFFFAOYSA-N 0.000 description 1
- MPLHNVLQVRSVEE-UHFFFAOYSA-N texas red Chemical compound [O-]S(=O)(=O)C1=CC(S(Cl)(=O)=O)=CC=C1C(C1=CC=2CCCN3CCCC(C=23)=C1O1)=C2C1=C(CCC1)C3=[N+]1CCCC3=C2 MPLHNVLQVRSVEE-UHFFFAOYSA-N 0.000 description 1
- 229940104230 thymidine Drugs 0.000 description 1
- FDRPZJWMPZUHBN-UHFFFAOYSA-N triazin-2-ium;chloride Chemical class Cl.C1=CN=NN=C1 FDRPZJWMPZUHBN-UHFFFAOYSA-N 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
- 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 modified ribooligonucleotide, that is to say a reagent for coupling at least one molecule to nucleic acids, in particular ribonucleic acids (RNA), a method for its production, its use and a reagent kit based on this modified ribooligonucleotide.
- This coupling reagent is a specifically modified ribooligonucleotide, which in principle consists of any number, but at least one ribonucleotide.
- this coupling reagent it is possible to use a variety of labels, in particular fluorescent labels, but also digoxigenin or biotin derivatives, or else other molecules, such as e.g. B. to couple proteins to nucleic acids, especially ribonucleic acids (RNA).
- nucleic acids The coupling of a wide variety of molecules to nucleic acids is a widely used method in molecular biology. Such methods are particularly important for labeling nucleic acids. They are used for protein-nucleic acid interaction studies, nucleic acid structure studies, for DNA and RNA sequencing or, for medical diagnostics of enormous importance, in hybridization methods, especially in-situ hybridization methods. Labeling has so far been carried out mainly on a radioactive basis with the aid of isotope-substituted nucleotides and corresponding enzymes. However, since radioactively labeled substances are quite expensive, handling them is not safe and the disposal of radioactive waste is problematic for ecological reasons, efforts have been made for some time to use alternative (i.e. non-radioactive) labeling options.
- RNA RNA molecule that is extended by one nucleotide and bears a radioactive label at the 3 "terminus. This method only allows the radioactive labeling of RNA.
- the object of the present invention is to develop a special ribooligonucleotide, i.e. H. to provide a reagent for coupling at least one molecule, more generally considered different substances, in particular a fluorescent marker, a biotin derivative, a digoxigenin derivative or a protein to nucleic acids, in particular ribonucleic acids (RNA), which avoids the disadvantages mentioned, i.e. its use on enzymatic Implementations is based and therefore has a high specificity that is easy to carry out and that allows many different substances to be coupled to nucleic acids. Furthermore, it is the object of the present invention to provide specific possible uses for the modified ribooligonucleotide, as well as a reagent kit based on this ribooligonucleotide.
- a special ribooligonucleotide i.e. H. to provide a reagent for coupling at least one molecule, more generally considered different substances, in particular a fluorescent marker,
- Nucleic acid is coupled, is preferably a fluorescent marker, for example a fluorescein derivative, but can also be a digoxigenin or biotin derivative or a protein, for example. Regardless of the nature of this molecule R 3 , it is referred to below as a marker for the sake of simplicity.
- a radioactive isotope is also possible, in contrast to the pCp conventionally used for radioactive labeling with the Coupling reagent according to the invention also "exotic" isotopes, such as 125 J can be introduced.
- the coupling reagent according to the invention consists of a ribooligonucleotide of any length in which a reactive group, in particular an amino group, is bonded directly or via a spacer group to one or more 3 ′′ phosphate groups.
- a sulfhydryl group can also be used as a reactive group "However, it is more sensitive and does not react with as many substituents as an amino group.
- Ri is a phosphate group
- R 2 is a nucleobase, especially cytidine
- R 3 is the molecule to be coupled
- a coupling reagent which also functions according to the invention is likewise obtained, but the conversion rates of the coupling reaction are up to 50% lower than when using cytidine.
- the ribooligonucleotide can be extended on its 3 "phosphate group with further nucleotides, which can also be substituted.
- the alkyl chain used as spacer contains no phosphate group and therefore also no R 4 radical.
- a hydrogen atom is then instead bonded to the carbon atom of the alkyl chain to which a phosphate group is bonded according to claims 1 and 2.
- An extension of the coupling reagent in the manner described above is then not possible and the coupling reagent has only a single marker molecule R 3 .
- RNA ligase especially the T4 RNA ligase.
- the minimum requirements of this enzyme must be Substrate is a 3 ", 5" ribonucleoside bisphosphate. Ribooligonucleotides which contain such a group at their 5 "end are bound by the RNA ligase to the 3" - OH group of any ribonucleic acid.
- the reagent can also be coupled to a DNA; all that is required is to attach a ribonucleotide to the 3 "end of the DNA before coupling.
- the reactive group which binds the marker is bonded to the 3 "phosphate group of the coupling reagent via a spacer containing phosphate.
- the spacer is an alkyl chain with a length of between 1 and 30 carbon atoms, to which a phosphate group can be bound.
- the coupling reagent can be extended further at this phosphate group of the spacer: Either by attaching another nucleoside to which a marker can in turn be bound (see formula I), or by directly introducing further marker molecules with a spacer (see formula II) .
- the length of the ribooligonucleotide can be selected as required and there is in principle the possibility of binding markers to any or all of the phosphate groups with the exception of the 5 "terminal phosphate group, a reagent is available with the coupling reagent according to the invention with which nucleic acids can be used in one step can be coupled with several markers, which, for example, gives a stronger signal, particularly in connection with in situ hybridization methods, which is a major advantage of the coupling reagent according to the invention, since it is very complex to obtain a signal amplification in conventional labeling methods.
- the coupling reagent is synthesized analogously to the automatic DNA synthesis. It is essential to the invention that the coupling reagent can be synthesized automatically with the aid of conventional DNA synthesizers, the synthesis cycle being suitably modified to the requirements of RNA synthesis.
- ribonucleotides are used as building blocks instead of deoxyribonucleotides and uracil is used instead of thymidine.
- the 2 "-OH group is protected by a protective group, for example a silyl group, during the reaction.
- the reaction time in RNA synthesis is approximately 10 minutes compared to approximately 3 minutes in DNA synthesis.
- ribooligonucleotide is synthesized according to the phosphoramidite method, which is described in detail by T. Atkinson and M. Smith (in: Oligonucleotide Synthesis; A Practical approach; MJ Gait (ed.) IRL Press, Oxford, Washington DC, 1984) on the solid phase from 3 "to 5".
- a reactive amino group is preferably introduced with the aid of a special amination reagent of the form (l-dimethoxytrityloxy-3-fluorenylmethoxycarbonylamino-propan-2-yl) - (2-cyanoethyl) - (N, N-diisopropyl) - phosphoramidite (for example from the company Glen Research [Sterling, Vancouver, Canada] available as 5 "-branched modifier C3).
- amination reagent results in a coupling reagent with a 3" -terminal nucleoside.
- This can be modified further, for example by oxidizing the 2 "- and 3" -OH groups to aldehyde groups.
- These aldehyde groups can react with amino groups to form a Schiff base. If the aldehyde groups are reacted with corresponding amino groups of enzymes, the enzyme is bound to the oligonucleotide.
- the terminal nucleoside is not modified, there is a risk that the 3 "OH group of this nucleoside reacts with the 5" phosphate group of the same type of molecule.
- the nucleoside can be split off at the 3 "end by means of ⁇ -elimination and the self-ligation can thereby be prevented.
- the reactive amino group can also be introduced with an amination reagent of the form (l-dimethoxytrityloxy-3-fluorenylmethoxycarbonylamino-propane-2-succinoyl) - aminoalkane (available, for example, from Glen Research as a 3 "amino-modifier-CPG), where directly a 3 "phosphate group according to formula (I) or (II) results.
- an amination reagent of the form (l-dimethoxytrityloxy-3-fluorenylmethoxycarbonylamino-propane-2-succinoyl) - aminoalkane (available, for example, from Glen Research as a 3 "amino-modifier-CPG), where directly a 3 "phosphate group according to formula (I) or (II) results.
- the ⁇ -elimination is saved if you do not want a terminal nucleoside.
- R 3 Various substances (R 3 ) which easily react with an amino group, such as fluorescent markers, for example a fluorescein derivative, or digoxigenin or biotin derivatives or else proteins, in particular nucleases, are then linked to the introduced amino group.
- Activated substituents can exist as isothiocyanates, isocyanates, as N-hydroxysuccinimide esters, p-nitrophenyl esters, sulfonic acid chlorides, triazine chlorides or as acid azides.
- the following substances are preferably used as markers: fluorescein succinimide ester, NBD-F (4-fluoro-7-nitrobenz-2-oxa-1,3-diazole), tetramethylrhodamine 5 (6) isothiocyanate, Texas red (sulphorhodamine-101-acid chloride) , Biotin succinimide ester, digoxygenin succinimide ester.
- proteins in particular nucleases
- this "crosslinking" of an enzyme to an oligonucleotide can in principle be carried out in the following ways: on the one hand, a free sulfhydryl group can be incorporated into the enzyme by incorporating a cysteine residue (see R. Zuckermann et al., Journal "J. Am. Chem. Soc.
- hetero cross-linking reagent eg N-succinimidyl 3- (2-pyridyldithio) propionate
- the succinimidyl residue of the hetero crosslinking reagent reacts with the amino group of the coupling reagent, causing the enzyme to cross the
- Crosslinking reagent is bound to the coupling reagent.
- Another way of introducing a free SH group into the corresponding enzyme is to chemically convert an amino group into an SH group (see Carlsson et al., Journal "Biochem. J”. 173, 723-737 (1978)) .
- the actual cross-linking takes place as described above.
- a third possibility of binding an enzyme to the coupling reagent is to use a homo cross-linking reagent which, in contrast to the hetero cross-linking reagent mentioned above, has two succinimidyl residues. It reacts both with the amino group of the coupling reagent and with an amino group of the enzyme.
- a phosphate group at the 5 "terminus of the ribooligonucleotide which is necessary for the reaction of the ribooligonucleotide with the nucleic acid to be labeled, is preferably carried out by means of a phosphorylation reagent of the form: 2- [2- (4,4" -dimethoxotrityloxy) ethylsulfonyl ] ethyl- (2-cyanoethyl) - (N, N-diisopropyl) - phosphoramidite (available from Glen Research as a chemical phosphorylation reagent).
- a 5 "phosphorylation is also possible with other methods, for example using ATP and the enzyme polynucleotide kinase. However, this method is extremely cumbersome and lengthy, especially on a larger scale.
- the coupling reagent according to the invention can be used with the aid of conventional DNA synthesizers are automatically synthesized.
- the synthesis of a coupling reagent of the form 5 "pCpCp fluorescein is explained in more detail below as an exemplary embodiment.
- RNA triplet was first produced from the following building blocks (direction: 5 "- 3") using the phosphoramidite method:
- the reagents were obtained from Glen Research, but are also available from other companies.
- RiboA-CPG are filled into a column and this is then sealed.
- the RNA synthesis cycle is started.
- the setting on the DNA synthesizer is: Tr off, auto. This means that the protective groups are split off and the product is split off from the carrier.
- the column after the reaction is rinsed with ethanol: NH 3/1: 3.
- the product thus obtained is lyophilized and then taken up again in 0.2 ml of 1 M tetraethylammonium fluoride in tetrahydrofuran. It is then incubated for 6 h at room temperature, as a result of which the protective groups on the ribose are split off. 0.3 ml of 1 M ammonium acetate solution, pH 5.3, is then added to this solution and diluted with 5 ml of water.
- the substance can be stored at -20 ° C or lyophilized for a long time without loss.
- the incubation medium contains:
- the incubation medium contains: - 50 ⁇ ⁇ labeled ribooligonucleotide (from b)
- the coupling reagent is used for coupling to nucleic acids.
- An enzyme namely an RNA ligase, preferably the T4 RNA ligase, catalyzes the bond between the 5 "phosphate end of the coupling reagent and the 3" OH end of the nucleic acid to be modified.
- the reaction is carried out in a special RNA ligase buffer which contains magnesium chloride, an organic solvent, ATP, coupling reagent, the nucleic acid to be modified and the RNA ligase at a slightly alkaline pH. This mixture is incubated at temperatures between 0 and 10 ° C. for 4 to 24 h and the modified nucleic acid is then extracted with phenol and precipitated with ethanol.
- RNA with fluorescein is carried out below using the coupling reagent, the synthesis of which was described in the example above.
- the total volume of the incubation medium contains 30 ⁇ :
- RNA ligase buffer 100 mM Hepes / KOH, pH 7.8; 40 mM magnesium chloride; 7 mM dithiothreitol; 20 ⁇ g / ml bovine serum albumin; 20% dimethyl sulfoxide
- a main application of the coupling reagent according to the invention is the coupling of labeling substances (R 3 ), in particular fluorescent markers, to nucleic acids.
- labeling substances R 3
- the straightforwardness of the method of binding marker substances to the coupling reagent and the coupling reagent to a nucleic acid makes it possible, for example in the form of a kit, to provide the user with the still unmodified coupling reagent and separately various marker substances. The user can then easily produce the coupling reagent as required and in the required modification as required. Since the coupling of the modified coupling reagent to the nucleic acid to be labeled is an enzymatic method, the user has a simple possibility of coupling any nucleic acids with markers of his choice very gently and with high specificity.
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Abstract
La présente invention concerne un ribo-oligonucléotide de formule (I) ou (II) dans lesquelles R1 désigne un groupe hydroxyle ou un groupe phosphate ou au moins un 3', 5'nucléotide-bisphosphate, R2 désigne une nucléobase, R3 est la molécule à coupler et R4 représente un atome d'hydrogène ou un nucléoside. Dans lesdites formules, m désigne un chiffre compris entre 1 et 100, et en particulier entre 2 et 5, n1 désigne 0 ou un chiffre compris entre 1 et 30, et en particulier 1, et n2 désigne 0 ou un chiffre compris entre 1 et 30, et en particulier 1. Le ribo-oligonucléotide convient pour le couplage de substances de marquage, en particulier des marqueurs fluorescents, mais également des protéines, en particulier des nucléases, avec catalyse d'une ligase ARN à des acides nucléiques. Ce ribo-oligonucléotide modifié peut être employé a) pour des procédés d'hybridation ou b) pour des études de la structure de l'ARN ou c) pour des études des interactions protéine-ARN ou d) pour des opérations particulières sur des acides nucléiques.
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
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DEP4239531.3 | 1992-11-25 | ||
DE19924239531 DE4239531A1 (de) | 1992-11-25 | 1992-11-25 | Reagenz zur Kupplung verschiedener Substanzen an Nukleinsäuren sowie Verfahren zu dessen Herstellung |
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WO1994012518A2 true WO1994012518A2 (fr) | 1994-06-09 |
WO1994012518A3 WO1994012518A3 (fr) | 1994-07-21 |
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PCT/DE1993/001101 WO1994012518A2 (fr) | 1992-11-25 | 1993-11-19 | Reactif pour le couplage de diverses substances a des acides nucleiques et procede pour sa preparation |
Country Status (2)
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DE (1) | DE4239531A1 (fr) |
WO (1) | WO1994012518A2 (fr) |
Cited By (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
GB2424479A (en) * | 2005-01-31 | 2006-09-27 | Agilent Technologies Inc | RNA labelling using RNA ligating enzymes |
US7544471B2 (en) | 2005-07-30 | 2009-06-09 | Agilent Technologies, Inc. | Preparing RNA from a wax-embedded tissue specimen |
US7700289B2 (en) | 2006-04-03 | 2010-04-20 | Agilent Technologies, Inc. | Method for labeling RNA |
US7718365B2 (en) | 2005-07-09 | 2010-05-18 | Agilent Technologies, Inc. | Microarray analysis of RNA |
US8076064B2 (en) | 2005-07-09 | 2011-12-13 | Agilent Technologies, Inc. | Method of treatment of RNA sample |
Families Citing this family (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
DE19954934A1 (de) * | 1999-11-16 | 2001-05-17 | Otto S Wolfbeis | Verfahren zur Solubilisierung von optischen Markern |
EP1136569A3 (fr) | 2000-03-24 | 2004-01-28 | Bayer Corporation | Sondes d'acides nucléiques qui ont des marqueurs non-nucléosidiques à haute hydrophilicité comprenant plusieurs autres marqueurs et leur utilisation |
US7572585B2 (en) | 2006-07-31 | 2009-08-11 | Agilent Technologies, Inc. | Enzymatic labeling of RNA |
Family Cites Families (9)
Publication number | Priority date | Publication date | Assignee | Title |
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FR2565996B1 (fr) * | 1984-06-15 | 1988-01-22 | Inst Nat Sante Rech Med | Acides nucleiques marques chimiquement, leur utilisation et necessaire pour sa mise en oeuvre |
US4757141A (en) * | 1985-08-26 | 1988-07-12 | Applied Biosystems, Incorporated | Amino-derivatized phosphite and phosphate linking agents, phosphoramidite precursors, and useful conjugates thereof |
US5352578A (en) * | 1989-02-15 | 1994-10-04 | Worcester Foundation For Experimental Biology | Method of separating oligonucleotides from a mixture |
DE3916871A1 (de) * | 1989-05-24 | 1990-11-29 | Boehringer Mannheim Gmbh | Modifiziertes phosphoramidit-verfahren zur herstellung von modifizierten nukleinsaeuren |
GB9009980D0 (en) * | 1990-05-03 | 1990-06-27 | Amersham Int Plc | Phosphoramidite derivatives,their preparation and the use thereof in the incorporation of reporter groups on synthetic oligonucleotides |
US5210015A (en) * | 1990-08-06 | 1993-05-11 | Hoffman-La Roche Inc. | Homogeneous assay system using the nuclease activity of a nucleic acid polymerase |
IL99068A (en) * | 1990-08-09 | 1998-01-04 | Genta Inc | Non-nucleotide binding reagents for oligomers |
WO1992003464A1 (fr) * | 1990-08-28 | 1992-03-05 | Microprobe Corporation | Synthese sur support solide d'oligonucleotides places en queue en position 3' par l'intermediaire d'une molecule de liaison |
DE4123540A1 (de) * | 1991-07-16 | 1993-01-21 | Boehringer Mannheim Gmbh | Immobilisierung von nukleinsaeuren |
-
1992
- 1992-11-25 DE DE19924239531 patent/DE4239531A1/de not_active Withdrawn
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1993
- 1993-11-19 WO PCT/DE1993/001101 patent/WO1994012518A2/fr active Application Filing
Cited By (7)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
GB2424479A (en) * | 2005-01-31 | 2006-09-27 | Agilent Technologies Inc | RNA labelling using RNA ligating enzymes |
GB2424479B (en) * | 2005-01-31 | 2009-02-25 | Agilent Technologies Inc | RNA labelling by ligation in the presence of DMSO |
US7541144B2 (en) | 2005-01-31 | 2009-06-02 | Agilent Technologies, Inc. | RNA labeling method |
US7718365B2 (en) | 2005-07-09 | 2010-05-18 | Agilent Technologies, Inc. | Microarray analysis of RNA |
US8076064B2 (en) | 2005-07-09 | 2011-12-13 | Agilent Technologies, Inc. | Method of treatment of RNA sample |
US7544471B2 (en) | 2005-07-30 | 2009-06-09 | Agilent Technologies, Inc. | Preparing RNA from a wax-embedded tissue specimen |
US7700289B2 (en) | 2006-04-03 | 2010-04-20 | Agilent Technologies, Inc. | Method for labeling RNA |
Also Published As
Publication number | Publication date |
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WO1994012518A3 (fr) | 1994-07-21 |
DE4239531A1 (de) | 1994-05-26 |
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