WO2007064291A1 - Procédé et composés permettant la synthèse de l'arn - Google Patents
Procédé et composés permettant la synthèse de l'arn Download PDFInfo
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- WO2007064291A1 WO2007064291A1 PCT/SE2006/050502 SE2006050502W WO2007064291A1 WO 2007064291 A1 WO2007064291 A1 WO 2007064291A1 SE 2006050502 W SE2006050502 W SE 2006050502W WO 2007064291 A1 WO2007064291 A1 WO 2007064291A1
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- WIPO (PCT)
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- tem
- rna
- synthesis
- nmr
- mhz
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- 0 **OC[C@@](C(C1O*)O)O[C@]1N(C=CC(N1)=O)C1=O Chemical compound **OC[C@@](C(C1O*)O)O[C@]1N(C=CC(N1)=O)C1=O 0.000 description 4
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
- C07H19/16—Purine radicals
- C07H19/167—Purine radicals with ribosyl as the saccharide radical
-
- 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
- C07H19/067—Pyrimidine radicals with ribosyl as the saccharide radical
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02P—CLIMATE CHANGE MITIGATION TECHNOLOGIES IN THE PRODUCTION OR PROCESSING OF GOODS
- Y02P20/00—Technologies relating to chemical industry
- Y02P20/50—Improvements relating to the production of bulk chemicals
- Y02P20/55—Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups
Definitions
- the present invention relates to RNA synthesis on solid supports.
- the purpose of the invention is to improve yield and purity of the products form such synthesis.
- a chemical entity defined in claim 2 is used for 2'-OH protection of the compounds in claim 1.
- Fig. 1 is a scheme (Scheme 1) showing synthesis of the 2'-O-Protecting groups used in oligo-RNA.
- Fig. 2 is a scheme (Scheme 4) showing protection of ribonucleoside at 2'-OH by the TEM group.
- Fig. 3 is PAGE pictures of crude products after deprotection.
- Fig. 4 shows RNA cleavage efficiency of pure RNA.
- Fig. 5 is a reversed-phase HPLC profile of products obtained by digestion.
- Fig. 6 shows solid-phase synthesis of 12 oligoRNAs.
- the present invention relates to a new 2'-OH Protecting Group for solid support RNA synthesis.
- RNA interference RNA interference
- siRNA short interferring RNA
- 2'-OH protecting groups can be classified to the following types depending upon the unblocking conditions: (1) Photosensitive groups such as Nbn (as shown in scheme I) 6 and Nbom, 7 (2) acid-labile acetal derivatives such as Mthp, 8 MDMP, 9 ' 10 Ctmp and Fpmp groups, 11 (3) base-labile groups such as Npes 12 , Fnebe and Nebe, 13 (4) reductively removable DTM group with labile S-S bond 14 , (5) the fluoride-labile groups such as tBDMS, 15"17 SEM, 18 or CEE, 19 which have been found to be useful in the solid-phase oligo-RNA synthesis.
- Photosensitive groups such as Nbn (as shown in scheme I) 6 and Nbom
- acid-labile acetal derivatives such as Mthp, 8 MDMP, 9 ' 10 Ctmp and Fpmp groups
- base-labile groups such as Npes 12 , Fnebe and Nebe
- An ideal 2'-OH protecting group should be 20 (1) easy to introduce, (2) achiral, (3) unable to migrate to vicinal 3'-OH, (4) completely stable under the conditions required for the assembly of the fully desired RNA sequence, as well as for its subsequent unblocking and release from the solid support. (5) It must be removable under conditions under which RNA is completely stable, and the 3' — >5' phosphodiester do not isomerize to 2' — »5' linkage. Though the 2'-protecting groups shown in Scheme 1 ( Figure 1) are widely used, none of them however completely fulfills the above criteria.
- the 2'-(9-CEM) can be unblocked through a ⁇ -elimination process with fluoride ion as the base. As expected, it is also cleaved to some extent during the ammonia treatment, which increases the possibility of chain cleavage, and may limit its further use for larger oligo-RNA synthesis.
- reducing the acidity of the ⁇ -proton to -CN group in 2'-0-CBM [2'-0-CH 2 -O-CH 2 -CH 2 -CN] 27 will increase its stability in the ammonia deprotection step.
- Acetyl (Ac), dimethylaminomethylene (Dmf) and phenoxyacetyl (Pac) were used to protect N 4 of cytosine, N 2 of guanosine and N 6 of adenosine, respectively. These exocyclic amino protected blocks and uridine were converted to their respective 5'-0-DMTr derivatives according to the published procedures.
- 3'-0-TEM can be isolated by silica gel column chromatography.
- the first isomer eluting from the column was the predominant product, 2'-0-TEM ribonucleosides 7a/7b/7c/7d in 26-38% yields.
- the second eluting isomer 8a/8b/8c/8d was isolated in 20-27% yields.
- the two isomers have been identified by NMR (see Section B).
- Reagents and Conditions (i) a, Bu 2 SnCl 2 , 'Pr 2 NEt, ClCH 2 CH 2 Cl, r.t, 1 h; b, compound 5, 80 0 C, 1 h. (ii) 2-cyanoethyl-N,N-diisopropylchlorophosphoramidite, 'Pr 2 NEt, CH 2 Cl 2 , r.t., 2 h. (iii) pimelic acid, EDAC, DMAP, pyridine, r.t., 4 h.
- 3 Jy 1 ⁇ of all alkylated compounds 7a - 12c follow Reese's rule, 35 in that the 3 Jy ⁇ ' of 2'-isomers are smaller than those of the 3'-isomers, while it is not the case for the T, 3'-isomeric silylated compounds 13a - 14c.
- a comparison of ⁇ r and ⁇ y however showed that for all the mono 2V3'-O-alkylated compounds 7a - 12c, alkylation causes an upfield shift of the proton attached to the site of 2' or 3'-O-alkylation.
- the value of ⁇ cr - ⁇ c 3' can be used as a more convenient identification parameter.
- the value of ⁇ cr - ⁇ cv of 2'-isomer is always larger than that of the corresponding 3 '-isomer.
- RNA synthesis (D) Automated RNA synthesis. We first synthesized U 12 under different conditions to optimize the synthesis cycle. This oligo was synthesized on an Applied Biosystems 392 DNA/RNA synthesizer with common DNA synthesis reagents. 2'-O-succinate-8a CPG was used as the solid support and 1.0 ⁇ mol RNA synthesis cycle was applied but with a modified coupling time. Average stepwise yield (ASWY), obtained by detritylation assay, was used to evaluate the synthesis efficiency.
- ASWY Average stepwise yield
- compound 15 was treated with neat Et 3 N.-3HF and IM TBAF/THF separately. It was found only IM TBAF/THF is an efficient reagent for the deprotection of the 2'-O-TEM group in that the deprotection was found to be complete in 5 min at room temperature.
- the oligo anchored solid support were first treated with 25% NH 3 /Me0H at room temperature for 20 h, then at 40 °C for 4 h to ensure the removal of the exocyclic amino protecting groups completely. After solvent removal and drying by coevaporation with dry THF, the samples were treated with IM TBAF/THF for 20 h at room temperature to make sure all 2'-0-TEM groups are deprotected. After desalting through a NAP-IO column and Sep-Pak column, the crude products were applied to PAGE or HPLC analysis. The PAGE pictures (see Figure 3) together with HPLC profiles show that the crude products of U 20 and U 38 are more than 80% pure.
- n-propylamine and 1% bis (2-mercaptoethyl) ether was used as scavenger for the active ⁇ , ⁇ -unsaturated compound (acrylonitrile), and thereby adduct formation was suppressed efficiently.
- n-propylamine also acts as a moderate base and can promote chain cleavage. So, with the hope to develop an improved scavenger, we tested several different deprotecting conditions for 2'-0-TEM with ON 3 and ON 4 as the substrates. The results are listed in Table 3.
- CH 3 NO 2 was reported as a scavenger for acrylonitrile in the presence of amine such as NH 3 ZMeCN, MeNH 2 ZH 2 O-EtOH-MeCN, 42 but it is not the case in the presence of TBAF in THF. On the contrary, when CH 3 NO 2 was used in conjunction with n-propylamine, it can inhibit the activity of n-propylamine.
- the 2'-0-TEM group is found to be stable in ammonia. Treating the oligo with NH 3 ZMeOH at room temperature for 20 h, then 40 0 C for 4 h
- RNA synthesis with the TEM strategy described above can indeed give crude product with high purity. To address whether this crude product is pure enough for biology research, a
- RNA 15nt long RNA (ON 12 in Table 2) was synthesized and, after deprotecting and desalting (see
- Figure 4 shows RNA cleavage efficiency of pure RNA and crude RNA (ON 12 in Fig 1) with RNase H (for the purity of pure RNA see the PAGE picture in Fig S5 in SI).
- Conditions of cleavage reactions pure RNA (0.1 ⁇ M) or crude RNA (0.1 ⁇ M) and complementary DNA (1 ⁇ M) in buffer containing 20 mM Tris-HCl
- the crude ON 12 was also subjected to digest by phosphodiesterase I (from Crotalus adamanteus Venom) and Shrimp Alkaline Phosphatase.
- the products were analyzed by RP-HPLC and the profile is shown in Figure 5.
- the crude products are completely digested to give pure nucleosides, which strong support that the oligo-RNA is in biologically active form and no modified base is present.
- HPLC condition C 18 RP column, 100*4.6mm, 1 ml/min, r.t, 0-10 min, buffer C ⁇ C/D 9/1, 10-35 min, buffer C/D 9/l ⁇ C/D 2/8.
- RNA synthesis can be carried out on standard solid support synthesizer with high average coupling yield and coupling time of only 120 second.
- the crude RNA obtained by of our 2'-O-TEM based strategy is of high purity, which, after desalting, can be directly used in the biological research without further purification, which is an important advantage over other strategies based on either 2'-0-TBDMS, 15'17 2'-0-TOM, 26 2'-0-CEM, 27 2'-O-ACE, 25 or 2'-O-Fpmp. 20
- MALDI-TOF mass spectra were recorded in positive ion mode for oligonucleotides and for other compounds as indicated.
- the mass spectrometer was externally calibrated with a peptide mixture using alpha-cyano-4-hydroxycinnamic acids as matrix.
- Buffer A 20 mM LiClO 4 , 20 mM NaOAc in H 2 O:CH 3 CN (9: 1), pH 6.5 with AcOH.
- Buffer B 600 mM LiClO 4 , 20 mM NaOAc in H 2 O:CH 3 CN (9:1), pH 6.5 with AcOH.
- Buffer C 0.1M TEAA in H 2 O:CH 3 CN (95:5).
- Buffer D 0.1M TEAA in H 2 O:CH 3 CN (50:50).
- JV ⁇ -Phenoxyacetyl-S'-O-DMTr adenosine (0.9 g, 1.2 mmol) was treated as described for 7a and 8a to give 7c (0.31 g, 26.4%) and 8c (0.265 g, 22.8%).
- N 2 -(N, iV-dimethylamino methylene)-5'-0-DMTr guanosine (4.5 g, 7 mxnol) was treated as described for 7a and 8a to give 7d (1.88 g, 31.4%) and 8d (1.60 g, 26.7%).
- the solid was suspended in dry pyridine (20 ml) with acetic anhydride (2.25 ml) and 4-dimethylaminopyridine (DMAP, 465 mg), shaken for 2 h at room temperature. After filtration, the solids were washed with pyridine, toluene, CH 2 Cl 2 , methanol, CH 2 Cl 2 , diethyl ether in turn and dried over P 2 O 5 under high vacuum.
- the loadings determined by detritylation assay, are 20-25 ⁇ mol/g.
- RNA synthesis and purification All the RNAs are assembled on Applied Biosystems 392 DNA/RNA synthesizer. All syntheses were carried out in trityl off mode. The synthesis cycle and reagents can be found in supplementary information.
- the solid supports were removed form the cartridges and treated with 25% NH 3 /MeOH (4ml) at room temperature for 20 h, then at 40 0 C for 4 h. Then the supernatant solutions were separated from the solid supports, evaporated to dryness.
- Escherichia coli RJNase H (5 units/ ⁇ L, specific activity 420000 units mg -1 , molecular weight 21000 g moF 1 ), T4 polynucleotide Kinase (30 units/ ⁇ L) and [7- 32 P]ATP were purchased from Amersham Pharmacia Biotech (Sweden).
- the pure 15 mer RNA (ON 12) was from IBABioTAGnology (received as a crude form and purified by PAGE, the purity is shown in Figure S5). Synthesis of the complementary DNA was carried out as previously described.
- the ON 12 was synthesized, deprotected, desalted by NAP-10 column and Sep-Pak cartridge just as upper description to give the crude ON 12, which was used directly for RNase H digestion.
- the RNA was 5'-end labeled with 32 P using T4 polynucleotide kinase, [7- 32 P]ATP by standard procedure.
- RNA and pure RNA were carried out according to the following procedure: target pure RNA (0.1 ⁇ M) or crude RNA (0.1 ⁇ M) (specific activity 70000 cpm) and 10-fold excess of complementary DNA (1 ⁇ M) were incubated in a buffer, containing 20 mM Tris-HCl (pH 8.0), 20 mM KCl, 10 mM MgCl 2 , 0.1 mM EDTA and 0.1 mM
- reaction components were pre-annealed in the reaction buffer by heating at 80 0 C for 4 min
- RNA synthesis on the solid-support the common synthetic strategy is to use a 4,4'-dimethoxytrityl (DMTr) group at the 5'-OH and a t-butyldimethylsilyl (TBDMS) group for 2'-OH protections.
- DMTr 4,4'-dimethoxytrityl
- TDMS t-butyldimethylsilyl
- R 4 -CH 3 or -CH 2 CH 2 CN
- Q (Q 1 ) CF 3 - ; (Q 2 ) CCI 3 - ; (Q 3 ) CBr 3 - ; (Q 4 ) MeS- ; (Q 3 ) CF 3 S- ; (Q 6 ) CF 3 S(O)- ; (Q 7 ) CF 3 SO 2 -; (Q 8 ) C 6 H 5 -S(O)- ; (Q 9 ) 0-Me-C 6 H 4 -S(O)- ; (Q 10 ) P-Me-C 6 H 4 -S(O)- ; (Q 11 ) /H-Me-C 6 H 4 -S(O)- ; (Q 12 ) 0-CI-C 6 H 4 -S(O)- ; (Q 13 ) P-Cl-C 6 H 4 -S(O)- ; (Q 14 ) /H-CI-C 6 H 4 -S(O)- ; (Q 15 )
- acetal protecting group such as FPMP
- ACE bis(2-acetoxyethyloxy)methyl
- TOM triisopropylsilyloxymethyl
- 2'-Acetal derivatives with electron-withdrawing substituents such as l-(2-cyanoethoxy) ethyl
- Gough et al. have introduced the fluoride-cleavable 4-nitrobenzyloxymethyl protecting group.
- electron-withdrawing substituents into formaldehyde acetal type protecting groups has also been introduced 11 . This approach has led to the development of a novel protecting group, 2-cyanoethoxymethyl (CEM), which has allowed synthesis of rather large oligo-RNA 11 .
- CEM 2-cyanoethoxymethyl
- the IM TBAF/THF with 10% n-propylamine and 1% bis (2-mercaptoethyl) ether remains to be the preferred reagent for deprotecting the 2'-0-TEM group from the oligo-RNA.
- the IM TBAF/THF with 10% morpholine at RT seems to be a more improved deprotection agent than IM TBAF/THF with 10% n-propylamine and 1% bis (2-mercaptoethyl) ether, which will be reported in a full paper.
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Abstract
La présente invention concerne 2-(4-tolylsulfonyl)ethoxymethyl (TEM) utilisé en tant que nouveau groupe de protection 2'-OH, lequel composé est utilisé pour la synthèse de l'ARN sur le support solide par chimie phosphoramidite. L'utilité du groupe 2'-O-TEM est illustrée par la synthèse de 12 différents oligo-ARN de différentes tailles (de 14 à 38nt de long). La production par couplage progressive varie de 97 à 99 % avec une durée de couplage optimisée de 120 secondes. Cette invention concerne également la synthèse de l'ensemble des quatre éléments constitutifs de phosphoramidite purs. Deux nouveaux paramètres fiables, dC2' - dc3' et dH2' - dH3' ont été suggérés pour la caractérisation des isomères 2'-O-TEM et 3'-O-TEM ainsi que pour d'autres dérivés ribonucléosides à protection mono 273 ' isomères. La caractéristique la plus frappante de ce mode de réalisation reside dans le fait que l'ARN brut préparé au moyen du procédé 2'-O-TEM décrit dans cette invention, est suffisamment pur (>90 %) pour permettre une recherche en biologie moléculaire sans étape de purification supplémentaire, ce qui permet d'obtenir facilement et à faible coût des oligo-ARN et, ainsi, d'économiser du temps et des ressources en laboratoire.
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Cited By (14)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN102574888A (zh) * | 2009-09-16 | 2012-07-11 | 株式会社启拉坚 | 用于rna及其衍生物的合成的新型保护基 |
US9394333B2 (en) | 2008-12-02 | 2016-07-19 | Wave Life Sciences Japan | Method for the synthesis of phosphorus atom modified nucleic acids |
US9598458B2 (en) | 2012-07-13 | 2017-03-21 | Wave Life Sciences Japan, Inc. | Asymmetric auxiliary group |
US9605019B2 (en) | 2011-07-19 | 2017-03-28 | Wave Life Sciences Ltd. | Methods for the synthesis of functionalized nucleic acids |
US9617547B2 (en) | 2012-07-13 | 2017-04-11 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant |
US9744183B2 (en) | 2009-07-06 | 2017-08-29 | Wave Life Sciences Ltd. | Nucleic acid prodrugs and methods of use thereof |
US9982257B2 (en) | 2012-07-13 | 2018-05-29 | Wave Life Sciences Ltd. | Chiral control |
US10144933B2 (en) | 2014-01-15 | 2018-12-04 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant having immunity induction activity, and immunity induction activator |
US10149905B2 (en) | 2014-01-15 | 2018-12-11 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant having antitumor effect and antitumor agent |
US10160969B2 (en) | 2014-01-16 | 2018-12-25 | Wave Life Sciences Ltd. | Chiral design |
US10322173B2 (en) | 2014-01-15 | 2019-06-18 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant having anti-allergic activity, and anti-allergic agent |
US10428019B2 (en) | 2010-09-24 | 2019-10-01 | Wave Life Sciences Ltd. | Chiral auxiliaries |
WO2021079617A1 (fr) | 2019-10-23 | 2021-04-29 | 住友化学株式会社 | Composé glycoside, composé amidite, et procédé de production d'un polynucléotide par utilisation desdits composés |
US11518780B2 (en) | 2019-07-31 | 2022-12-06 | Shiyue Fang | Sensitive oligonucleotide synthesis using sulfur-based functions as protecting groups and linkers |
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Cited By (26)
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US9394333B2 (en) | 2008-12-02 | 2016-07-19 | Wave Life Sciences Japan | Method for the synthesis of phosphorus atom modified nucleic acids |
US10329318B2 (en) | 2008-12-02 | 2019-06-25 | Wave Life Sciences Ltd. | Method for the synthesis of phosphorus atom modified nucleic acids |
US9695211B2 (en) | 2008-12-02 | 2017-07-04 | Wave Life Sciences Japan, Inc. | Method for the synthesis of phosphorus atom modified nucleic acids |
US10307434B2 (en) | 2009-07-06 | 2019-06-04 | Wave Life Sciences Ltd. | Nucleic acid prodrugs and methods of use thereof |
US9744183B2 (en) | 2009-07-06 | 2017-08-29 | Wave Life Sciences Ltd. | Nucleic acid prodrugs and methods of use thereof |
EP2479182A1 (fr) * | 2009-09-16 | 2012-07-25 | Chiralgen, Ltd. | Nouveau groupe protecteur pour synthétiser de l'arn et dérivé de celui-ci |
EP2479182A4 (fr) * | 2009-09-16 | 2013-05-08 | Chiralgen Ltd | Nouveau groupe protecteur pour synthétiser de l'arn et dérivé de celui-ci |
US8470987B2 (en) | 2009-09-16 | 2013-06-25 | Chiralgen, Ltd. | Protective group for synthesis of RNA and derivative |
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US9617547B2 (en) | 2012-07-13 | 2017-04-11 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant |
US9982257B2 (en) | 2012-07-13 | 2018-05-29 | Wave Life Sciences Ltd. | Chiral control |
US10322173B2 (en) | 2014-01-15 | 2019-06-18 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant having anti-allergic activity, and anti-allergic agent |
US10149905B2 (en) | 2014-01-15 | 2018-12-11 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant having antitumor effect and antitumor agent |
US10144933B2 (en) | 2014-01-15 | 2018-12-04 | Shin Nippon Biomedical Laboratories, Ltd. | Chiral nucleic acid adjuvant having immunity induction activity, and immunity induction activator |
US10160969B2 (en) | 2014-01-16 | 2018-12-25 | Wave Life Sciences Ltd. | Chiral design |
US11518780B2 (en) | 2019-07-31 | 2022-12-06 | Shiyue Fang | Sensitive oligonucleotide synthesis using sulfur-based functions as protecting groups and linkers |
WO2021079617A1 (fr) | 2019-10-23 | 2021-04-29 | 住友化学株式会社 | Composé glycoside, composé amidite, et procédé de production d'un polynucléotide par utilisation desdits composés |
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KR20220086589A (ko) | 2019-10-23 | 2022-06-23 | 스미또모 가가꾸 가부시끼가이샤 | 배당체 화합물, 아미다이트 화합물, 및 이들 화합물을 사용한 폴리뉴클레오티드의 제조 방법 |
JP7606972B2 (ja) | 2019-10-23 | 2024-12-26 | 住友化学株式会社 | 配糖体化合物、アミダイト化合物、およびこれら化合物を用いたポリヌクレオチドの製造方法 |
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