Current Protocols in Nucleic Acid Chemistry最新文献_第5页

An Improved Strategy for the Chemical Synthesis of 3',5'-Cyclic Diguanylic Acid. 3',5'-环二鸟苷酸化学合成的改进策略。

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-06-01 Epub Date: 2019-04-10 DOI: 10.1002/cpnc.84

Andrzej Grajkowski, Mayumi Takahashi, Tomasz Kaczyński, Suresh C Srivastava, Serge L Beaucage

{"title":"An Improved Strategy for the Chemical Synthesis of 3',5'-Cyclic Diguanylic Acid.","authors":"Andrzej Grajkowski, Mayumi Takahashi, Tomasz Kaczyński, Suresh C Srivastava, Serge L Beaucage","doi":"10.1002/cpnc.84","DOIUrl":"10.1002/cpnc.84","url":null,"abstract":"The physiological functions of c-di-GMP and its involvement in many key processes led to its recognition as a major and ubiquitous bacterial second messenger. Aside from being a bacterial signaling molecule, c-di-GMP is also an immunostimulatory molecule capable of inducing innate and adaptive immune responses through maturation of immune mammalian cells. Given the broad biological functions of c-di-GMP and its potential applications as a nucleic-acid-based drug, the chemical synthesis of c-di-GMP has drawn considerable interest. An improved phosphoramidite approach to the synthesis of c-di-GMP is reported herein. The synthetic approach is based on the use of a 5'-O-formyl protecting group, which can be rapidly and chemoselectively cleaved from a key dinucleotide phosphoramidite intermediate to enable a cyclocondensation reaction leading to a fully protected c-di-GMP product in a yield ∼80%. The native c-di-GMP is isolated, after complete deprotection, in an overall yield of 36% based on the commercial ribonucleoside used as starting material. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581608/pdf/nihms-1019201.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37140008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An Efficient Synthesis of 5-Aminopropargyl-Pyrimidine-5'-O-Triphosphates Through Palladium-Catalyzed Sonogashira Coupling. 钯催化Sonogashira偶联高效合成5-氨基丙炔嘧啶-5′- o -三磷酸盐。

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-06-01 Epub Date: 2019-03-18 DOI: 10.1002/cpnc.81

Muthian Shanmugasundaram, Annamalai Senthilvelan, Anilkumar R Kore

{"title":"An Efficient Synthesis of 5-Aminopropargyl-Pyrimidine-5'-O-Triphosphates Through Palladium-Catalyzed Sonogashira Coupling.","authors":"Muthian Shanmugasundaram, Annamalai Senthilvelan, Anilkumar R Kore","doi":"10.1002/cpnc.81","DOIUrl":"https://doi.org/10.1002/cpnc.81","url":null,"abstract":"The utilization of 5-aminopropargyl nucleotide serves as a versatile molecular biology tool for the introduction of functional groups into a nucleic acid target of interest by using in-vitro enzymatic incorporation method. This article describes a simple, reliable, general, and efficient two-step chemical method for the synthesis of 5-(3-aminopropargyl)-2'-deoxycytidine-5'-O-triphosphate, 5-(3-aminopropargyl)-cytidine-5'-O-triphosphate, 5-(3-aminopropargyl)-2'-deoxyuridine-5'-O-triphosphate, and 5-(3-aminopropargyl)-uridine-5'-O-triphosphate, starting from the corresponding pyrimidine triphosphate. The first step involves regioselective C-5 iodination of pyrimidine triphosphate using N-iodosuccinimide and sodium azide. In the second step, propargylamine is coupled to the iodo-pyrimidine using the palladium-catalyzed Sonogashira reaction, producing good yields of highly pure (>99.5% HPLC) 5-aminopropargyl-pyrimidine-5'-O-triphosphate. In this approach, the palladium-catalyzed Sonogashira coupling reaction is highly chemoselective and does not involve protection and deprotection. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.81","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37066648","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: 0

Issue Information TOC 问题信息TOC

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-02-26 DOI: 10.1002/cpnc.65

引用次数: 0

Affinity Isolation of Defined Genomic Fragments Cleaved by Nuclease S1-based Artificial Restriction DNA Cutter 基于核酸酶s1的人工限制性DNA切割器切割的基因组片段的亲和分离

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-02-12 DOI: 10.1002/cpnc.76

Arivazhagan Rajendran, Narumi Shigi, Jun Sumaoka, Makoto Komiyama

引用次数: 2

6-Phenylpyrrolocytidine: An Intrinsically Fluorescent, Environmentally Responsive Nucleoside Analogue 6-苯基吡咯胞苷:一种内在荧光，环境响应核苷类似物

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-02-06 DOI: 10.1002/cpnc.75

Sung Ju Cho, Arash Ghorbani-Choghamarani, Yoshio Saito, Robert H.E. Hudson

引用次数: 4

Artificial Restriction DNA Cutter Using Nuclease S1 for Site-Selective Scission of Genomic DNA 利用核酸酶S1进行基因组DNA位点选择性切割的人工限制性DNA切割器

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-02-05 DOI: 10.1002/cpnc.72

Arivazhagan Rajendran, Narumi Shigi, Jun Sumaoka, Makoto Komiyama

引用次数: 1

Facile Modifications at the C4 Position of Pyrimidine Nucleosides via In Situ Amide Activation with 1H-Benzotriazol-1-yloxy-tris(dimethyl-amino)phosphonium Hexafluorophosphate h -苯并三唑-1-酰氧基-三(二甲基-氨基)六氟磷酸磷酸原位酰胺活化对嘧啶核苷C4位的易修饰

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-01-28 DOI: 10.1002/cpnc.73

Hari K. Akula, Mahesh K. Lakshman

{"title":"Facile Modifications at the C4 Position of Pyrimidine Nucleosides via In Situ Amide Activation with 1H-Benzotriazol-1-yloxy-tris(dimethyl-amino)phosphonium Hexafluorophosphate","authors":"Hari K. Akula, Mahesh K. Lakshman","doi":"10.1002/cpnc.73","DOIUrl":"10.1002/cpnc.73","url":null,"abstract":"Two approaches for C4 modifications of silyl-protected thymidine, 2′-deoxyuridine, and 3′-azido-2′,3′-dideoxythymidine (AZT) are described. In both, nucleoside amide activation with 1H-benzotriazol-1-yloxy-tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and DBU yields O4-(benzotriazol-1-yl) derivatives. These in situ–formed intermediates are reacted with various nucleophiles, resulting in C4 modifications. In the two-step, one-pot approach, the O4-(benzotriazol-1-yl) nucleoside intermediates are initially produced by reactions of the nucleosides with BOP and DBU in THF. This step is fast and typically complete within 30 min. Subsequently, the O4-(benzotriazol-1-yl) derivatives are reacted with nucleophiles, such as aliphatic and aromatic amines, thiols, and alcohols, under appropriate conditions. Workup, isolation, and purification lead to the desired C4-modified pyrimidine nucleosides in good to excellent yields. In the one-step approach, the nucleosides are reacted with BOP and DBU, in the presence of the nucleophile (only aliphatic and aromatic amines, and thiols have been tested). Where comparisons are possible, the one-step approach is generally superior. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.73","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36947191","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

Synthesis and Characterization of Site-Specific O6-Alkylguanine DNA-Alkyl Transferase-Oligonucleotide Crosslinks 位点特异性o6 -烷基鸟嘌呤dna -烷基转移酶-寡核苷酸交联的合成与表征

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-01-18 DOI: 10.1002/cpnc.74

Pratibha P. Ghodke, Matthew E. Albertolle, Kevin M. Johnson, F. Peter Guengerich

{"title":"Synthesis and Characterization of Site-Specific O6-Alkylguanine DNA-Alkyl Transferase-Oligonucleotide Crosslinks","authors":"Pratibha P. Ghodke, Matthew E. Albertolle, Kevin M. Johnson, F. Peter Guengerich","doi":"10.1002/cpnc.74","DOIUrl":"https://doi.org/10.1002/cpnc.74","url":null,"abstract":"O6-Alkylguanine DNA-alkyltransferase (AGT), a DNA repair protein, can form crosslinks with DNA. The AGT-DNA crosslinks are known to be mutagenic when AGT is heterologously expressed in Escherichia coli, as well as in mammalian cells. To understand the biological consequences, reliable access to AGT-oligonucleotide crosslinks is needed. This article describes the synthesis and characterization of site-specific AGT-oligonucleotide crosslinks at the N2-position of deoxyguanosine and N6-position of deoxyadenosine. We developed a post-oligomerization strategy for the synthesis of propargyl-modified oligonucleotides. Copper-catalyzed azide-alkyne cycloaddition was used as a key step to obtain the iodoacetamide-linked oligonucleotides, which serve as good electrophiles for the crosslinking reaction with cysteine-145 of the active site of AGT. Trypsinization of AGT and hydrolysis of oligonucleotides, combined with analysis by liquid chromatography-tandem mass spectrometry, was utilized to confirm the nucleobase-adducted peptides. This method provides a useful strategy for the synthesis and characterization of site-specific DNA-protein crosslinks, which can be further used to understand proteolytic degradation–coupled DNA repair mechanisms. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.74","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92300732","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: 5

Synthesis of Fluorescence Turn-On DNA Hybridization Probe Using the ^DEA tC 2'-Deoxycytidine Analog. 用DEA tC 2’-脱氧胞苷类似物合成荧光开启DNA杂交探针。

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-12-01 Epub Date: 2018-10-18 DOI: 10.1002/cpnc.59

M Benjamin Turner, Brooke A Anderson, George N Samaan, Michael Coste, Dillon D Burns, Byron W Purse

{"title":"Synthesis of Fluorescence Turn-On DNA Hybridization Probe Using the DEA tC 2'-Deoxycytidine Analog.","authors":"M Benjamin Turner, Brooke A Anderson, George N Samaan, Michael Coste, Dillon D Burns, Byron W Purse","doi":"10.1002/cpnc.59","DOIUrl":"10.1002/cpnc.59","url":null,"abstract":"DEA tC is a tricyclic 2'-deoxycytidine analog that can be incorporated into oligonucleotides by solid-phase synthesis and that exhibits a large fluorescence enhancement when correctly base-paired with a guanine base in a DNA-DNA duplex. The synthesis of DEA tC begins with 5-amino-2-methylbenzothiazole and provides the DEA tC nucleobase analog over five synthetic steps. This nucleobase analog is then silylated using N,O-bis(trimethylsilyl)acetamide and conjugated to Hoffer's chlorosugar to provide the protected DEA tC nucleoside in good yield. Following protective-group removal and chromatographic isolation of the β-anomer, dimethoxytritylation and phosphoramidite synthesis offer the monomer for solid-phase DNA synthesis. Solid-phase DNA synthesis conditions using extended coupling of the DEA tC amidite and a short deprotection time are employed to maximize efficiency. By following the protocols described in this unit, the DEA tC fluorescent probe can be synthesized and can be incorporated into any desired synthetic DNA oligonucleotide. © 2018 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.59","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36669637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Synthesis of Trinucleotide Building Blocks in Solution and on Solid Phase. 固相和溶液中三核苷酸合成的研究。

Current Protocols in Nucleic Acid Chemistry Pub Date : 2018-12-01 Epub Date: 2018-10-30 DOI: 10.1002/cpnc.60

Ruth Suchsland, Bettina Appel, Sabine Müller

引用次数: 4