Current Protocols in Nucleic Acid Chemistry最新文献_第8页

A Simple Chemical Synthesis of Sugar Nucleoside Diphosphates in Water 糖核苷二磷酸在水中的简单化学合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-16 DOI: 10.1002/0471142700.nc1312s54

Hidenori Tanaka, Yayoi Yoshimura, Ole Hindsgaul

引用次数: 3

Molecular Modeling of Nucleic Acid Structure: Energy and Sampling 核酸结构的分子建模:能量和采样

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-16 DOI: 10.1002/0471142700.nc0708s54

Christina Bergonzo, Rodrigo Galindo-Murillo, Thomas E. Cheatham III

引用次数: 3

DNA Interstrand Cross-Link Formation Using Furan as a Masked Reactive Aldehyde 用呋喃作为屏蔽活性醛形成DNA链间交联

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-16 DOI: 10.1002/0471142700.nc0512s54

Lieselot L.G. Carrette, Ellen Gyssels, Annemieke Madder

引用次数: 6

2′-Hydroxy Protection of Ribonucleosides as 2-Cyano-2,2-Dimethylethanimine-N-Oxymethyl Ethers in Solid-Phase Synthesis of RNA Sequences 核糖核苷作为2-氰-2,2-二甲基乙胺- n -氧甲基醚在RNA序列固相合成中的2′-羟基保护作用

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-16 DOI: 10.1002/0471142700.nc0322s54

Jacek Cieślak, Cristina Ausín, Andrzej Grajkowski, Serge L. Beaucage

{"title":"2′-Hydroxy Protection of Ribonucleosides as 2-Cyano-2,2-Dimethylethanimine-N-Oxymethyl Ethers in Solid-Phase Synthesis of RNA Sequences","authors":"Jacek Cieślak, Cristina Ausín, Andrzej Grajkowski, Serge L. Beaucage","doi":"10.1002/0471142700.nc0322s54","DOIUrl":"10.1002/0471142700.nc0322s54","url":null,"abstract":"The reaction of 2′-O-aminooxymethylribonucleosides with 2-cyano-2-methyl propanal leads to the formation of stable and yet reversible 2′-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl)ribonucleosides in post-purification yields of 54% to 82%. Phenoxyacetylation of the exocyclic amino functions of these ribonucleosides proceeds in yields of 74% to 89%, and subsequent 5′-O-dimethoxytritylation and 3′-O-phosphitylation of the corresponding N-phenoxyacetylated ribonucleosides provide the fully protected ribonucleoside phosphoramidite monomers in isolated yields of 69% to 88%. These ribonucleoside phosphoramidites are employed in solid-phase synthesis of three chimeric RNA sequences, each differing in purine/pyrimidine content. The stepwise coupling efficiency of the ribonucleoside phosphoramidites (as 0.15 M solutions in acetonitrile) averages 99% over a coupling time of 180 s when 5-benzylthio-1H-tetrazole is used as an activator. Upon completion of RNA chain assembly, removal of the nucleobase- and phosphate-protecting groups and release of sequences from the solid support are carried out under standard basic conditions. Finally, the 2′-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl) protective groups are cleaved from the RNA sequences by treatment with 0.5 M tetra-n-butylammonium fluoride in dry DMSO for 24 to 48 hr at 55°C without releasing RNA-alkylating side-products. Characterization of the fully deprotected RNA sequences by PAGE, enzymatic hydrolysis, and MALDI-TOF mass spectrometry confirms the identity and high quality of these sequences. Curr. Protoc. Nucleic Acid Chem. 54:3.22.1-3.22.28. © 2013 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/0471142700.nc0322s54","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32101463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Molecular Modeling of Nucleic Acid Structure 核酸结构的分子模拟

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-16 DOI: 10.1002/0471142700.nc0705s54

Rodrigo Galindo-Murillo, Christina Bergonzo, Thomas E. Cheatham III

引用次数: 14

Fluorous-Assisted Synthesis of (E)-5-[3-Aminoallyl]-Uridine-5′-O-Triphosphate 氟辅助合成(E)-5-[3-氨基烯丙基]-尿苷-5 ' - o -三磷酸

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-15 DOI: 10.1002/0471142700.nc0133s60

Anilkumar R. Kore, Bo Yang, Balasubramanian Srinivasan

引用次数: 0

Symmetrical Diamidate Prodrugs of Nucleotide Analogues for Drug Delivery 对称二酯前药的核苷酸类似物的药物传递

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-15 DOI: 10.1002/0471142700.nc1506s60

Fabrizio Pertusati, Christopher McGuigan, Michaela Serpi

{"title":"Symmetrical Diamidate Prodrugs of Nucleotide Analogues for Drug Delivery","authors":"Fabrizio Pertusati, Christopher McGuigan, Michaela Serpi","doi":"10.1002/0471142700.nc1506s60","DOIUrl":"10.1002/0471142700.nc1506s60","url":null,"abstract":"The use of pronucleotides to circumvent the well-known drawbacks of nucleotide analogs has played a significant role in the area of antiviral and anticancer drug delivery. Several motifs have been designed to mask the negative charges on the phosphorus moiety of either nucleoside monophosphates or nucleoside phosphonates, in order to increase their hydrophobicity and allow entry of the compound into the cell. Among them the bis-amidate analogs, having two identical amino acids as masking groups through a P–N bond, represent a more recent approach for the delivery of nucleotide analogs, endowed with antiviral or anticancer activity. Different synthetic strategies are commonly used for preparing phosphorodiamidates of nucleosides. In this protocol, we would like to focus on the description of the synthetic methodology that in our hand gave the best results using 2′-3′-didehydro-2′-3′-dideoxythymidine (d4T, Stavudine) as model nucleoside. A second strategy for preparing diamidates of nucleoside phosphonates will be reported using {[2-(6-amino-9 H-purin-9-yl)ethoxy]methyl}phosphonic acid (PMEA, adefovir) as model substrate. © 2015 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/0471142700.nc1506s60","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33116805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Microwave-Assisted Phosphitylation of DNA and RNA Nucleosides and Their Analogs 微波辅助DNA和RNA核苷及其类似物的磷酸化

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-15 DOI: 10.1002/0471142700.nc0219s60

Tim Efthymiou, Ramanarayanan Krishnamurthy

引用次数: 2

Characterization of Thioether-Linked Protein Adducts of DNA Using a Raney-Ni-Mediated Desulfurization Method and Liquid Chromatography-Electrospray-Tandem Mass Spectrometry 用raney - ni介导的脱硫法和液相色谱-电喷雾-串联质谱法表征DNA的硫醚连接蛋白加合物

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-15 DOI: 10.1002/0471142700.nc1015s60

Goutam Chowdhury, F. Peter Guengerich

引用次数: 0

A New Nucleic Acid Prodrug Responsive to High Thiol Concentration: Synthesis of 2′-O-Methyldithiomethyl-Modified Oligonucleotides by Post-Synthetic Modification 一种对高硫醇浓度有反应的新型核酸前药:合成后修饰合成2 ' - o -甲基二硫甲基修饰寡核苷酸

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-15 DOI: 10.1002/0471142700.nc0463s62

Yosuke Ochi, Osamu Nakagawa, Junsuke Hayashi, Shun-ichi Wada, Hidehito Urata

{"title":"A New Nucleic Acid Prodrug Responsive to High Thiol Concentration: Synthesis of 2′-O-Methyldithiomethyl-Modified Oligonucleotides by Post-Synthetic Modification","authors":"Yosuke Ochi, Osamu Nakagawa, Junsuke Hayashi, Shun-ichi Wada, Hidehito Urata","doi":"10.1002/0471142700.nc0463s62","DOIUrl":"10.1002/0471142700.nc0463s62","url":null,"abstract":"This unit describes the synthesis of 2′-O-methyldithiomethyluridine-containing oligonucleotides, which can be deprotected to yield the parental oligoribonucleotides under high concentrations of glutathione similar in cytoplasm. The 2′-O-methyldithiomethyl group is sensitive to reductive conditions, so that it is incompatible to 3′-O-phosphoramidite modification in nucleosides. Thus, a novel post-synthetic approach to obtain 2′-O-methyldithiomethyluridine-containing oligonucleotides was developed, in which 2′-O-(2,4,6-trimethoxybenzylthiomethyl)uridine-modified oligonucleotides are readily converted by treatment with dimethyl(methylthio)sulfonium tetrafluoroborate to the 2′-O-methyldithiomethyluridine-modified oligonucleotides. The 2′-O-methyldithiomethyluridine-modified oligonucleotides are readily and cleanly converted to the parental oligonucleotides under high thiol conditions, such as 10 mM glutathione and dithiothreitol. © 2015 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/0471142700.nc0463s62","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34183139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1