- Resolved P-metalated nucleoside phosphoramidites
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The synthesis of resolved P-metalated nucleoside phosphoramidites is described. These rare compounds were initially prepared with gold as the metal center; however, the gold can be removed using basic phosphines or solid-supported triphenylphosphine. Treatment of the free nucleoside phosphoramidite with a platinum source generated a unique platinated dinucleoside species with a diastereomeric ratio of >99:1.
- Miller, Erica J.,Garcia, Kevin J.,Holahan, Erin C.,Ciccarelli, Rosa M.,Bergin, Rachel A.,Casino, Stephanie L.,Bogaczyk, Tyler L.,Krout, Michael R.,Findeis, Peter M.,Stockland, Robert A.
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- RETRACTED ARTICLE: Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases
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Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.
- Tran, Ai,Zheng, Song,White, Dawanna S.,Curry, Alyson M.,Cen, Yana
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p. 11818 - 11826
(2020/11/18)
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- Oxidative substitution of boranephosphonate diesters as a route to post-synthetically modified DNA
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The introduction of modifications into oligonucleotides is important for a large number of applications in the nucleic acids field. However, the method of solid-phase DNA synthesis presents significant challenges for incorporating many useful modifications that are unstable to the conditions for preparing synthetic DNA. Here we report that boranephosphonate diesters undergo facile nucleophilic substitution in a stereospecific manner upon activation by iodine. We have subsequently used this reactivity to post-synthetically introduce modifications including azides and fluorophores into DNA by first synthesizing boranephosphonate-linked 2′-deoxyoligonucleotides and then treating these oligomers with iodine and various nucleophiles. In addition, we show that this reaction is an attractive method for preparing stereodefined phosphorus-modified oligonucleotides. We have also examined the mechanism of this reaction and show that it proceeds via an iodophosphate intermediate. Beyond nucleic acids synthesis, due to the ubiquity of phosphate derivatives in natural compounds and therapeutics, this stereospecific reaction has many potential applications in organophosphorus chemistry.
- Paul, Sibasish,Roy, Subhadeep,Monfregola, Luca,Shang, Shiying,Shoemaker, Richard,Caruthers, Marvin H.
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supporting information
p. 3253 - 3264
(2015/03/30)
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- Microwave-assisted preparation of nucleoside-phosphoramidites
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Microwave-assisted phosphitylation of sterically hindered nucleosides is demonstrated to be an efficient method for the preparation of corresponding phosphoramidites (otherwise onerous under standard conditions) and is shown to be general in its applicability. the Partner Organisations 2014.
- Meher,Efthymiou,Stoop,Krishnamurthy
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supporting information
p. 7463 - 7465
(2014/07/07)
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- Studies on the synthesis of neamine-dinucleosides and neamine-PNA conjugates and their interaction with RNA
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Two types of neamine derivatives, neamine-dinucleotide conjugates 8a-g and neamine-PNA conjugates 12a-c and 14a-d, were synthesized. Compound 8a-g were synthesized by the condensation of azido-neamine with dinucleotide-5′-carboxylic acids, followed by reduction and deprotection. Compound 12a-c and 14a-d were synthesized by the similar strategy. The binding affinities of conjugates 8a-g, 12a-c, and 14a-d towards 16S RNA, 18S RNA, and TAR RNA were evaluated by SPR. It indicates that conjugates 12a-c and 14a-d interact with 16S, 18S RNA at the same level as that of neamine, 14a and 14d show about twofold binding affinities to TAR RNA compared to that of neamine. However, the neamine-dinucleotide conjugates 8a-g exhibit very weak binding affinities to 16S, 18S, and TAR RNA, computer modelling results that negative-negative electrostatic repulsion of phosphate group in compound 8a-g and RNA leads to a sharp decrease of the binding affinities compared with that of neamine, neamine-nucleoside and neamine-PNA conjugates.
- Mei, Hui,Xing, Lei,Cai, Li,Jin, Hong-Wei,Zhao, Peng,Yang, Zhen-Jun,Zhang, Liang-Ren,Zhang, Li-He
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supporting information; experimental part
p. 5355 - 5358
(2009/07/18)
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- PROCESS FOR PRODUCING PHOSPHOROAMIDITE
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The present invention provides high purity phosphoroamidite products by reducing the amount of impurities of triphosphite which has been additionally produced according to the conventional technique.Phosphoroamidites can be obtained with high purity such that the excess reaction is suppressed by using a reaction activator hardly generating triphosphite.According to the present invention, phosphoroamides can be obtained with high purity, which has heretofore been difficult to suppress the generation of impurities of triphosphite.
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Page/Page column 8
(2008/06/13)
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- Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity
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Due to the development in the field of RNA synthesis over the past decade of years, preparation of RNA oligonucleotides longer than 50 nucleotides is possible today. In this report, we describe the chemical preparation of a branched RNA molecule with RNA cleavage activity consisting of 81 nucleotides. It is derived from the hairpin ribozyme, a small catalytic RNA occurring in nature. The hairpin ribozyme consists of two separately folded domains (loop A and loop B domain), which can be joined in a number of different ways without loss of activity. In the construct presented here, 2′-deoxy-N4-(6- hydroxyhexyl)-5-methylcytidine was introduced to connect the loop B domain with the loop A domain via an artificial branch. The synthesized branched RNA is able to catalyze the cleavage of a number of suitable substrates. Compared with the corresponding non-branched reverse-joined ribozyme it cleaves its substrates only 5-fold slower. Surprisingly, no ligation activity could be detected.
- Ivanov, Sergei A.,Volkov, Eugene M.,Oretskaya, Tatiana S.,Müller, Sabine
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p. 9273 - 9281
(2007/10/03)
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- Methods of producing phosphitylated compounds
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Provided are methods of producing phosphitylated compounds, including 3′-O-phosphoramidites, comprising the step of reacting a hydroxyl-containing compound with a phosphitylating agent in the presence of a phosphitylation activator selected from the group consisting of: (1) acid-base complexes derived from an amine base of Formula I 1wherein R, R1, and R2 are independently C1-C10 alkyl, C1-C10 cycloalkyl, C1-C10 aryl, C1-C10 aralkyl, C1-C10 heteroalkyl, or C1-C10 heteroaryl; (2) acid-base complexes derived from an amine base of Formula II 2wherein R3, R4, R5, R6, and R7 are independently hydrogen, C1-C10 alkyl, C1-C10 cycloalkyl, C1-C10 aryl, C1-C10 aralkyl, C1-C10 heteroalkyl, or C1-C10 heteroaryl, and at least one of R3, R4, R5 R6, and R7 is not hydrogen.; (3) acid-base complexes derived from a diazabicyclo amine base; (4) zwitterionic amine complexes; and (5) combinations of two or more thereof, to produce a phosphitylated compound.
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- Antisense molecules and method of controlling expression of gene function by using the same
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An antisense molecule which acts on both directions of the inhibition and expression of a gene function and is capable of on-off switching of a gene function appropriately depending on the external factors (orientation controlling factors); and a method for reversibly controlling the expression of a gene function by using the antisense molecule. Such an antisense molecule, which has at least one sugar-base moiety consisting of sugar and a purine or pyrimidine base bonded thereto via a glucoside bond, can bind to a mRNA/gene and/or dissociate therefrom under the orientation control of the base moiety in the molecule by the orientation controlling factors.
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- Nucleoside derivatives
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Novel nucleoside derivatives represented by the following general formula (1): 1wherein X is(are) the same or different and each represents a pyrimidine or purine base or a derivative thereof, Y-and Y′ are the same or different and each represents at least one amino acid or amino acid derivative selected from the group consisting of serine, threonine, ornithine, aspartic acid, glutamic acid, lysine, arginine, cysteine, methionine, δ-hydroxylysine, N-aminoethylglycine, N-aminoethylserine, N-aminoethyllysine, N-aminoethylornithine, N-aminoethylaspartic acid, N-aminoethylglutamic acid, homoglutamic acid, β-thiocarbonylaspartic acid, γ-thiocarbonylglutamic acid, and δ-thiocarbonylhomoglutamic acid, R1 represents a hydrogen atom or a hydroxyl group, A represents a single bond or a carbonyl or thiocarbonyl group, 1 is an integer of 0 to 5, and n is an integer of 1 to 100.
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- Improved process for the preparation of nucleosidic phosphoramidites using a safer and cheaper activator
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A new, simplified commercial process for the preparation of nucleosidic phosphoramidites, key raw materials for the automated solid-supported synthesis of oligonucleotide-based drugs, was developed. Phosphitylation of a variety of protected nucleosidic derivatives (1-4) with a small excess of 2-cyanoethyl-N,N,N′,N′-tetraisopropyl phosphoramidite (5, bis-reagent) and pyridinium trifluoroacetate (Py·TFA) as the activator in an appropriate solvent at room temperature formed 75-96% of desired nucleosidic phosphoramidite products in less than 2 h. An efficient nonaqueous work-up has been developed to further streamline the isolation of moisture-sensitive P(III) nucleosidic compounds. The key finding is the use of Py·TFA, which is effective, inexpensive, stable, less acidic (pKa 5.2) than 1H-tetrazole, nontoxic, safe, and highly soluble in organic solvents. The reaction mechanism for phosphitylation with Py TFA as an activator has also been studied. An improved, robust, and versatile process for the preparation of nucleotide phosphoramidites under very concentrated reaction conditions was developed to support commercial manufacture of oligonucleotide-based drugs.
- Sanghvi, Yogesh S.,Guo, Zhiqiang,Pfundheller, Henrik M.,Converso, Antonella
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p. 175 - 181
(2013/09/07)
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- Synthesis of analogues of oligonucleotides; synthesis of unprotected C-linked di- and tri-nucleotides
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The Wittig reaction between the N-benzyloxymethylthymidine-derived ylide 25 and the aldehyde 16 followed by hydrogenolysis gives access to the unprotected C-linked dinucleotide 20 on a multi-gram scale. Oxidation of the dinucleotide gives the aldehyde 27 which is condensed with the ylide 25 to give the unprotected bis-C-linked trinucleotide 29 after hydrogenolysis. The mono-C-linked trinucleotide 44 is prepared by oxidation of the dinucleotide ester 34 to the aldehyde 36 which is condensed with the ylide 25 followed by hydrogenolysis to give the mono-C-linked trinucleotide ester 38. This intermediate is also prepared from the C-linked dinucleotide 20 by conversion into the phosphoramidite 41 which is coupled with 3-acetylthymidine 15 to give the mono-C-linked trinucleotide phosphite 42. Oxidation and deprotection give the phosphate triester 38. Treatment of 38 with methanolic ammonia gives the fully unprotected mono-C-linked trinucleotide 44.
- Mellor, Ben J.,Thomas, Eric J.
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p. 747 - 757
(2007/10/03)
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- Novel unique catalytic activating reagents in synthesis of biophosphates via the phosphoramidite route
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Trimethylchlorosilane (TMSCI) and 2,4-dinitrophenol are remarkably efficient activators in reaction of P(III) amides with nucleosides to give P(III) esters in excellent yield.
- Dabkowski, Wojciech,Tworowska, Izabela,Michalski, Jan,Cramer, Friedrich
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p. 1639 - 1644
(2007/10/03)
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- Facile synthesis of oligodeoxyribonucleotides via the phosphoramidite method without nucleoside base protection
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A facile synthesis of oligodeoxyribonucleotides via the phosphoramidite approach without base protection of the building blocks has been developed; it relies on the use of imidazolium triflate as a promoter for the condensation of a nucleoside phosphoramidite and a nucleoside. In the solution phase, the condensation is accomplished in a highly O-selective manner by using equimolar amounts of an N-free nucleoside phosphoramidite and an N-unblocked nucleoside to give, after oxidation with bis(trimethylsilyl)peroxide or with tert-butyl hydroperoxide, a dinucleoside phosphate in > 95% yield. In the solid-phase synthesis, which requires an excess amount of the phosphoramidite for the condensation, deoxyadenosine and deoxycytidine undergo N-phosphitylation to some extent. The undesired product, however, can be converted to the N-free derivative by brief treatment with benzimidazolium triflate in methanol. Thus the overall process allows the chemoselective formation of internucleotide linkage. The oligomers prepared by this N-unprotected solid-phase approach include (5')GTCACGACGTTGTAAAACGAC(3') (21mer), (5')CAGGAAACAG-CTATGACCATG(3') (21mer), (5')CAAGTTGATGAACAATACTTCATACCTAAACT(3') (32mer), and (5')TATGGGCCTTTGATAGGATGCTCACCGAGCAAAACCAAGAACAA-CCAGGAGATTTATT(3') (60mer), which are provided in excellent quality. PCR amplification of DNAs using the crude 21mers as primers is also demonstrated.
- Hayakawa, Yoshihiro,Kataoka, Masanori
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p. 12395 - 12401
(2007/10/03)
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- Trimethylchlorosilane: A novel activating reagent in nucleotide synthesis via the phosphoramidite route
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Trimethylchlorosilane (TMSCl) is a remarkably efficient activator in the reaction of phosphorus(III) amides with nucleosides to give phosphorus(III) esters in excellent yield.
- Dabkowski, Wojciech,Tworowska, Izabela,Michalski, Jan,Cramer, Friedrich
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p. 877 - 878
(2007/10/03)
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- A novel phosphitylating reagent for in situ generation of deoxyribonucleoside phosphoramidites
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A new phosphitylating reagent, 2-cyanoethoxy(N,N-diisopropylamino)3-nitro-1,2,4-triazolylphosphine (1), has been prepared and effectively used in in situ generation of 5'-DMT-nucleoside phosphoramidites and automated syntheses of oligonucleotides.
- Zhang, Zhaoda,Tang, Jin Yan
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p. 331 - 334
(2007/10/02)
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- First synthesis of carbocyclic oligothymidylates
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5'-O-(dimethoxytrityl)-(+)-carbocyclic thymidine 1 is converted into different 3'-substituted intermediates 2a-c following standard procedures. From these compounds stereochemically pure carbocyclic oligothymidylates 4 are obtained using solid phase synthetic methods.
- Szemzo,Szecsi,Sagi,Otvos
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p. 1463 - 1466
(2007/10/02)
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- Some Steric Aspects of Synthesis of Oligoribonucleotides by Phosphoramidite Approach on Solid Support
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The influence of 2'-O-substituents (i.e. methyl, tetrahydropyranyl, tert-butyldimethylsilyl) on the chemical synthesis of oligoribonucleotides by phosphoramidite approach on solid support is described and compared with respective 2'-deoxynucleoside derivative.The observations on reactivity of these different 2'-O-protected derivatives at phosphatilation and condensation steps show their strong hindrance dependence.Some other aspects like reactivity of tetrahydropyranyl diastereoisomers, 3'- and 2'-O-phosphoramidites and some chemical properties of 2'-O-(tert-butyldimethylsilyl) protecting group are also presented.
- Kierzek, Ryszard,Rozek, Marek,Markiewicz, Wojciech T.
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p. 507 - 516
(2007/10/02)
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- NEW APPROACH TO THE SYNTHESIS OF DEOXYNUCLEOSIDE-PHOSPHORAMIDITE DERIVATIVES
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A new method for the synthesis of deoxyribonucleoside-phosphoramidite via an intermediate, 5'-O-dimethoxytritylthymidine-3'-O-diisopropylamino-phosphorochloridite, is reported.By using this method, several deoxyribonucleoside phosphoramidite derivatives with different protecting groups at phosphorus including P-S and P-N bond besides P-O bond were synthesized.
- Tanaka, Toshiki,Tamatsukuri, Sigeru,Ikehara, Morio
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p. 199 - 202
(2007/10/02)
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- New Approach to the Synthesis of Deoxyribonucleoside Phosphoramidite Derivatives
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The deoxyribonucleoside phosphoramidites with various protecting groups at phosphorus have been prepared rapidly in good yields in one-pot reaction from bis(diisopropylamino)chlorophosphine as a new phosphitylating agent without isolation of bis(diisopropylamino)alkoxyphosphines.
- Hamamoto, Shoji,Takaku, Hiroshi
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p. 1401 - 1404
(2007/10/02)
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- POLYMER-SUPPORTED SYNTHESIS OF DEOXYOLIGONUCLEOTIDES USING IN SITU PREPARED DEOXYNUCLEOSIDE 2-CYANOETHYL PHOSPHORAMIDITES
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The easily acessibile reagent 2-cyanoethyl-bis(diisopropylamino)phosphoramidite is shown to be suitable for the in-situ, 1H-tetrazole catalysed, preparation of d-nucleoside-3'-phosphoramidites.THe latter compounds could be applied successfuly as building blocks in a solid-phase DNA synthesis using an automated DNA synthesizer.
- Nielsen, J.,Marugg, J. E.,Taagaard, M.,Boom, J. H. van,Dahl, O.
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- A NEW AND VERSATILE APPROACH TO THE PREPARATION OF VALUABLE DEOXYNUCLEOSIDE 3'-PHOSPHITE INTERMEDIATES
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The easily accessible and crystalline monofunctional phosphitylating reagent bis-(diisopropylamino)chlorophosphine has been used for the synthesis of phosphoramidites and H-phosphonates of d-nucleosides and, also, the formation of 3'-5'-internucleotidic phosphonate bonds.
- Marugg, J. E.,Burik, A.,Tromp, M.,Marel, G. A. van der,Boom, J. H. van
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p. 2271 - 2274
(2007/10/02)
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- β-CYANOETHYL N,N-DIALKYLAMINO/N-MORPHOLINOMONOCHLORO PHOSPHOAMIDITES, NEW PHOSPHITYLATING AGENTS FACILITATING EASE OF DEPROTECTION AND WORK-UP OF SYNTHESIZED OLIGONUCLEOTIDES
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β-Cyanoethyl monochlorophosphoamidites of the secondary amines N,N-dimethylamine, N,N-diisopropylamine and morpholine have been prepared which showed quantitative phosphitylation of the protected deoxynucleosides.The phosphitylated deoxynucleosides have successfully been used in the formation of internucleotidic bonds. β-Cyanoethyl nucleoside-3'-N,N-diisopropylphosphoamidites have saticfactorily been used for the synthesis of the oligodeoxynucleotide d(CGGTACCG).
- Sinha, N. D.,Biernat, J.,Koester, H.
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p. 5843 - 5846
(2007/10/02)
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