Current Protocols in Nucleic Acid Chemistry最新文献_第9页

Synthesis of γ-Phosphate-Labeled and Doubly Labeled Adenosine Triphosphate Analogs γ-磷酸标记和双标记三磷酸腺苷类似物的合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-15 DOI: 10.1002/0471142700.nc1314s60

Stephan M. Hacker, Moritz Welter, Andreas Marx

引用次数: 2

Probing RNA Folding Pathways by RNA Fingerprinting 利用RNA指纹技术探测RNA折叠途径

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.36

Sarah A. Woodson

引用次数: 0

Determining Functional Aptamer-Protein Interaction by Biolayer Interferometry 生物层干涉法测定功能适配体-蛋白质相互作用

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.18

Xinhui Lou, Martin Egli, Xianbin Yang

{"title":"Determining Functional Aptamer-Protein Interaction by Biolayer Interferometry","authors":"Xinhui Lou, Martin Egli, Xianbin Yang","doi":"10.1002/cpnc.18","DOIUrl":"10.1002/cpnc.18","url":null,"abstract":"Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol). We also report on the protocol for the affinity screening of a panel of anti-thrombin RNA aptamers with a single phosphorodithioate (PS2) modification, whereby the position of the modification along the RNA backbone is varied systematically (Support Protocol). The PS2 modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphodiester backbone linkage. The PS2-modified RNAs are nuclease resistant and several in vitro and in vivo assays have demonstrated their biological activity. For example, combining the PS2 with the 2′-OMe modification affords increased loading of modified small interfering RNA (siRNA) duplexes into the RNA-induced silencing complex (RISC) as well as enhanced gene-silencing antitumor activity. © 2016 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.18","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50902276","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: 20

Vibration Ball Milling for the Synthesis of 5′-Thioadenosine 5′-Pyrophosphate (P′→5′) Adenosine (dASppA) 振动球磨法合成5′-硫代腺苷5′-焦磷酸(P′→5′)腺苷(dASppA)

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.37

Olga Eguaogie, Joseph S. Vyle

{"title":"Vibration Ball Milling for the Synthesis of 5′-Thioadenosine 5′-Pyrophosphate (P′→5′) Adenosine (dASppA)","authors":"Olga Eguaogie, Joseph S. Vyle","doi":"10.1002/cpnc.37","DOIUrl":"10.1002/cpnc.37","url":null,"abstract":"Using vibration ball milling, 5′-chloro-5′-deoxyadenosine (CldA) reacts cleanly with 4-methoxybenzyl mercaptan (MobSH), under basic conditions, to the corresponding thioether (MobSdA), which is isolated following precipitation and trituration. Under acidic conditions, in a one-pot, two-step process, MobSdA is transformed into 5′-deoxy-5′-(5-nitropyridyl-2-disulfanyl)-adenosine (NPySSdA). Michaelis-Arbuzov (M-A) reaction of NPySSdA with tris(trimethylsilyl) phosphite proceeds to completion within 30 min as determined by 31P NMR, and the persilylated M-A product thus formed can be stored in solution under anhydrous conditions at room temperature for several days (in contrast, the anionic phosphorothiolate monoester is labile to hydrolysis). Following evaporation, mechanochemical mixing of the crude M-A product with the nucleotide donor adenosine 5′-monophosphomorpholidate under acidic activation in the presence of additional water gives rapid hydrolytic desilylation and phosphate coupling, so that essentially complete reaction is observed after 90 min and dASppA isolated following C-18 reversed phase HPLC and desalting (>99% pure as determined by monitoring at 260 nm). © 2017 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":"70 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.37","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35419190","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

Synthesis of the Phosphoramidite Units for Benzene-Glycol Nucleic Acid 苯乙二醇核酸酰胺磷酸基的合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.38

Yusuke Maeda, Nazuki Niwa, Yoshihito Ueno

引用次数: 0

Nucleoside-O-Methyl-(H)-Phosphinates: Novel Monomers for the Synthesis of Methylphosphonate Oligonucleotides Using H-Phosphonate Chemistry 核苷- o -甲基-(H)-膦酸盐:用H-膦酸盐化学合成甲基膦酸寡核苷酸的新单体

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.35

Ondřej Kostov, Ondřej Páv, Ivan Rosenberg

引用次数: 1

Practical Synthesis of 4′-Thioribonucleosides from L-Arabinose via Novel Reductive Ring-Contraction Reaction and Pummerer-Type Thioglycosylation 以l -阿拉伯糖为原料，通过新型还原环收缩反应和pummer型硫代糖基化合成4′-硫代核糖核苷

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.45

Hideaki Wakamatsu, Kozue Nitta, Nozomi Shoji, Yoshihiro Natori, Yukako Saito, Yuichi Yoshimura

引用次数: 1

Synthesis of 4′-Selenoribonucleosides, the Building Blocks of 4′-SelenoRNA, Using a Hypervalent Iodine 利用高价碘合成4′-硒核苷，作为4′-硒核苷的组成部分

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.34

Noriko Saito-Tarashima, Masashi Ota, Noriaki Minakawa

引用次数: 4

3′-O-Caged 2′-Deoxynucleoside Triphosphates for Light-Mediated, Enzyme-Catalyzed, Template-Independent DNA Synthesis 3 ' -O-Caged 2 ' -脱氧核苷三磷酸光介导，酶催化，模板非依赖性DNA合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.41

Anu Stella Mathews, Haikang Yang, Carlo Montemagno

{"title":"3′-O-Caged 2′-Deoxynucleoside Triphosphates for Light-Mediated, Enzyme-Catalyzed, Template-Independent DNA Synthesis","authors":"Anu Stella Mathews, Haikang Yang, Carlo Montemagno","doi":"10.1002/cpnc.41","DOIUrl":"10.1002/cpnc.41","url":null,"abstract":"Synthesis, purification, and characterization of 3′-O-caged 2′-deoxyribonucleoside triphosphates (dNTPs), namely 3′-O-(2-nitrobenzyl)-2′-deoxy ribonucleoside triphosphates (NB-dNTPs) and 3′-O-(4,5-dimethoxy-2-nitrobenzyl)-2′-deoxy ribonucleoside triphosphates (DMNB-dNTPs), are discussed in detail. A total of eight 3′-O-caged dNTPs are synthesized with specific protocols depending on the nitrogenous base on the first carbon, i.e., adenine, guanine, thymine, and cytosine, as well as the photo-cleavable group, i.e, 2-nitrobenzyl and 4,5- dimethoxy-2-nitrobenzyl, to be attached in the 3′-O position. The purification of the synthesized compounds is done using ion-exchange and flash chromatography; this is followed by structural confirmation by nuclear magnetic resonance (NMR) and mass spectroscopy (MS). The efficiency of the designed compounds is tested by conducting and evaluating UV-cleaving experiments at 365 nm with proton NMR and LC-MS curves. Finally, the application of the 3′-O-cagged dNTPs in template-independent, enzyme-catalyzed, photo-mediated oligonucleotide synthesis is demonstrated. © 2017 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":"71 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.41","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35686182","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: 10

Palladium-Catalyzed Synthesis of (E)-5-(3-Aminoallyl)-Uridine-5′-O-Triphosphates 钯催化合成(E)-5-(3-氨基烯丙基)-尿苷-5′- o -三磷酸酯

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-02-13 DOI: 10.1002/cpnc.42

Muthian Shanmugasundaram, Annamalai Senthilvelan, Anilkumar R. Kore

引用次数: 1