Current Protocols in Nucleic Acid Chemistry最新文献_第3页

Synthesis of 2′-Fluorinated Northern Methanocarbacyclic (2′-F-NMC) Nucleosides and Their Incorporation Into Oligonucleotides 2′-氟化北甲碳环(2′-F-NMC)核苷的合成及其与寡核苷酸的结合

Current Protocols in Nucleic Acid Chemistry Pub Date : 2020-01-27 DOI: 10.1002/cpnc.103

Masaaki Akabane-Nakata, Pawan Kumar, Namrata D. Erande, Shigeo Matsuda, Muthiah Manoharan

{"title":"Synthesis of 2′-Fluorinated Northern Methanocarbacyclic (2′-F-NMC) Nucleosides and Their Incorporation Into Oligonucleotides","authors":"Masaaki Akabane-Nakata, Pawan Kumar, Namrata D. Erande, Shigeo Matsuda, Muthiah Manoharan","doi":"10.1002/cpnc.103","DOIUrl":"10.1002/cpnc.103","url":null,"abstract":"This article describes chemical synthesis of 2′-fluorinated Northern methanocarbacyclic (2′-F-NMC) nucleosides and phosphoramidites, based on a bicyclo[3.1.0]hexane scaffold bearing all four natural nucleobases (U, C, A, and G), and their incorporation into oligonucleotides by solid-supported synthesis. This synthesis starts from commercially available cyclopent-2-en-1-one to obtain the fluorinated carbocyclic pseudosugar intermediate (S.13), which can be converted to the uridine intermediate by condensation with isocyanate, followed by cyclization, and to adenine and guanine precursors by microwave-assisted reactions. All four 2′-F-NMC phosphoramidites are synthesized from S.13 in a convergent approach, and the monomers are used for synthesis of 2′-F-NMC-modified oligonucleotides. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Preparation of fluorinated carbocyclic pseudosugar intermediateBasic Protocol 2: Preparation of 2′-F-NMC uridine and cytidine phosphoramiditesBasic Protocol 3: Preparation of 2′-F-NMC adenosine phosphoramiditeBasic Protocol 4: Preparation of 2′-F-NMC guanosine phosphoramiditeBasic Protocol 5: Synthesis of oligonucleotides containing 2ʹ-F-NMC","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37583222","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

Synthesis of 4-Cyanoindole Nucleosides, 4-Cyanoindole-2ʹ-Deoxyribonucleoside-5ʹ-Triphosphate (4CIN-TP), and Enzymatic Incorporation of 4CIN-TP into DNA 4-氰吲哚核苷、4-氰吲哚-2′-脱氧核糖核苷-5′-三磷酸(4CIN-TP)的合成及4CIN-TP在DNA中的酶促结合

Current Protocols in Nucleic Acid Chemistry Pub Date : 2020-01-07 DOI: 10.1002/cpnc.101

Kellan T. Passow, Nicole M. Antczak, Shana J. Sturla, Daniel A. Harki

{"title":"Synthesis of 4-Cyanoindole Nucleosides, 4-Cyanoindole-2ʹ-Deoxyribonucleoside-5ʹ-Triphosphate (4CIN-TP), and Enzymatic Incorporation of 4CIN-TP into DNA","authors":"Kellan T. Passow, Nicole M. Antczak, Shana J. Sturla, Daniel A. Harki","doi":"10.1002/cpnc.101","DOIUrl":"10.1002/cpnc.101","url":null,"abstract":"4-Cyanoindole-2ʹ-deoxyribonucleoside (4CIN) is a fluorescent isomorphic nucleoside analogue with superior spectroscopic properties in terms of Stokes shift and quantum yield in comparison to the widely utilized isomorphic nucleoside analogue, 2-aminopurine-2ʹ-deoxyribonucleoside (2APN). Notably, when inserted into single- or double-stranded DNA, 4CIN experiences substantially less in-strand fluorescence quenching compared to 2APN. Given the utility of these properties for a spectrum of research applications involving oligonucleotides and oligonucleotide-protein interactions (e.g., enzymatic processes, DNA hybridization, DNA damage), we envision that additional reagents based on 4-cyanoindole nucleosides may be widely utilized. This protocol expands on the previously published synthesis of 4CIN to include synthetic routes to both 4-cyanoindole-ribonucleoside (4CINr) and 4-cyanoindole-2ʹ-deoxyribonucleoside-5ʹ-triphosphate (4CIN-TP), as well as a method for the enzymatic incorporation of 4CIN-TP into DNA by a polymerase. These methods are anticipated to further enable the utilization of 4CIN in diverse applications involving DNA and RNA oligonucleotides. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Synthesis of 4-cyanoindole-2ʹ-deoxyribonucleoside (4CIN) and 4CIN phosphoramidite 4Basic Protocol 2: Synthesis of 4-cyanoindole-ribonucleoside (4CINr)Basic Protocol 3: Synthesis of 4-cyanoindole-2ʹ-deoxyribonucleoside-5ʹ-triphosphate (4CIN-TP)Basic Protocol 4: Steady state incorporation kinetics of 2AP-TP and 4CIN-TP by a DNA polymerase","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37519093","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

Copper-Catalyzed Huisgen 1,3-Dipolar Cycloaddition Tailored for Phosphorothioate Oligonucleotides 专为硫代寡核苷酸设计的铜催化Huisgen 1,3-偶极环加成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-12-29 DOI: 10.1002/cpnc.102

Malgorzata Honcharenko, Dmytro Honcharenko, Roger Stromberg

{"title":"Copper-Catalyzed Huisgen 1,3-Dipolar Cycloaddition Tailored for Phosphorothioate Oligonucleotides","authors":"Malgorzata Honcharenko, Dmytro Honcharenko, Roger Stromberg","doi":"10.1002/cpnc.102","DOIUrl":"10.1002/cpnc.102","url":null,"abstract":"An efficient method for attachment of a variety of reporter groups to oligonucleotides (ONs) is copper (I) [Cu(I)]-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition (“click reaction”). However, in the case of ONs with phosphorothioate modifications as internucleosidic linkages (PS-ONs), this conjugation method has to be adjusted to be compatible with the sulfur-containing groups. The method described here is adapted for PS-ONs, utilizes solid-supported ONs, and implements the Cu(I) bromide dimethyl sulfide complex (CuBr × Me2S) as a mediator for the click reaction. The solid-supported ONs can be readily transformed into “clickable ONs” by on-line addition of an alkyne-containing linker that subsequently can react with an azido-containing moiety (e.g., a peptide) in the presence of CuBr × Me2S. © 2019 by John Wiley & Sons, Inc.Basic Protocol 1: Conjugation on solid supportSupport Protocol: Removal of 4,4′-dimethoxytrityl group from amino linkerBasic Protocol 2: Removal of protecting groups and cleavage from solid supportBasic Protocol 3: HPLC purification","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.102","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37497513","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

Issue Information TOC 问题信息TOC

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-12-19 DOI: 10.1002/cpnc.68

引用次数: 0

Highly Regioselective Methylation of Guanosine Nucleotides: An Efficient Synthesis of 7-Methylguanosine Nucleotides 鸟苷核苷酸的高度区域选择性甲基化:7‐甲基鸟苷核苷酸的高效合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-10-09 DOI: 10.1002/cpnc.100

Annamalai Senthilvelan, Muthian Shanmugasundaram, Anilkumar R. Kore

引用次数: 0

Issue Information TOC 问题信息TOC

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-09-17 DOI: 10.1002/cpnc.67

引用次数: 0

Synthesis of Monovalent N-Acetylgalactosamine Phosphoramidite for Liver-Targeting Oligonucleotides 肝靶向寡核苷酸单价N-乙酰氨基半乳糖的合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-09-15 DOI: 10.1002/cpnc.99

Tsuyoshi Yamamoto, Chisato Terada, Koki Kashiwada, Asako Yamayoshi, Mariko Harada-Shiba, Satoshi Obika

{"title":"Synthesis of Monovalent N-Acetylgalactosamine Phosphoramidite for Liver-Targeting Oligonucleotides","authors":"Tsuyoshi Yamamoto, Chisato Terada, Koki Kashiwada, Asako Yamayoshi, Mariko Harada-Shiba, Satoshi Obika","doi":"10.1002/cpnc.99","DOIUrl":"10.1002/cpnc.99","url":null,"abstract":"Ligand-targeted drug delivery (LTDD) has emerged as an attractive option in the field of oligonucleotide drugs following the great success of N-acetylgalactosamine (GalNAc)–conjugated siRNA and antisense oligonucleotides. GalNAc is a well-known ligand of the asialoglycoprotein receptor (ASGPR), and is classified as a C-type lectin associated with the metabolism of desialylated glycoproteins. This article describes the synthesis of a non-nucleosidic monovalent GalNAc phosphoramidite—a useful reagent for facilitating the conjugation of GalNAc epitopes into oligonucleotides using DNA synthesizers—together with some important caveats. The monomeric GalNAc consists of three parts: (1) a GalNAc moiety, (2) a linker moiety, and (3) a trans-4-hydroxyprolinol (tHP) branch point. The GalNAc moiety and the tHP moiety are coupled via a condensation reaction to prepare the monovalent GalNAc phosphoramidite. © 2019 by John Wiley & Sons, Inc.Basic Protocol 1: Synthesis of N-acetylgalactosamine ligandBasic Protocol 2: Preparation of trans-4-hydroxyprolinol building blockBasic Protocol 3: Preparation of GalNAc phosphoramidite","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.99","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43651743","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

Full Pre-Steady-State Kinetic Analysis of Single Nucleotide Incorporation by DNA Polymerases DNA聚合酶整合单核苷酸的全预稳态动力学分析

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-08-28 DOI: 10.1002/cpnc.98

Marleen Renders, Jean-Marie Frère, Dominique Toye, Piet Herdewijn

引用次数: 1

Synthesis of N2-Aryl-2′-Deoxyguanosine Modified Phosphoramidites and Oligonucleotides N2‐芳基‐2′‐脱氧鸟苷修饰的磷酰胺和寡核苷酸的合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-08-01 DOI: 10.1002/cpnc.93

Pratibha P. Ghodke, P. I. Pradeepkumar

{"title":"Synthesis of N2-Aryl-2′-Deoxyguanosine Modified Phosphoramidites and Oligonucleotides","authors":"Pratibha P. Ghodke, P. I. Pradeepkumar","doi":"10.1002/cpnc.93","DOIUrl":"10.1002/cpnc.93","url":null,"abstract":"The N2-position of 2′-deoxyguanosine (N2-position in dG) is well known for forming carcinogenic minor groove DNA adducts, which originate from environmental pollutants, chemicals, and tobacco smoke. The N2-dG DNA adducts have strong implications on biological processes such as DNA replication and repair and may, therefore, result in genomic instability by generating mutations or even cell death. It is crucial to know the role of DNA polymerases when they encounter the N2-dG damaged site in DNA. To get detailed insights on the in vitro DNA damage tolerance or bypass mechanism, there is a need to synthetically access N2-dG damaged DNAs. This article describes a detailed protocol of the synthesis of N2-aryl-dG modified nucleotides using the Buchwald-Hartwig reaction as a main step and incorporation of the modified nucleotides into DNA. In Basic Protocol 1, we focused on the synthesis of five different N2-dG modified phosphoramidites with varying bulkiness (benzyl to pyrenyl). Basic Protocol 2 describes the details of synthesizing N2-dG modified oligonucleotides employing the standard solid phase synthesis protocol. This strategy provides robust synthetic access to various modifications at the N2-position of dG; the modified dGs serve as good substrates to study translesion synthesis and repair pathways. Overall data presented in this article are based on earlier published reports. © 2019 by John Wiley & Sons, Inc.","PeriodicalId":10966,"journal":{"name":"Current Protocols in Nucleic Acid Chemistry","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpnc.93","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41461003","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: 2

Synthesis of Poly(ADP-ribose) Monomer Containing 2′-O-α-D-Ribofuranosyl Adenosine 含2′‐O‐α‐D‐核糖呋喃基腺苷的聚(ADP‐核糖)单体的合成

Current Protocols in Nucleic Acid Chemistry Pub Date : 2019-07-16 DOI: 10.1002/cpnc.92

Sergey N. Mikhailov, Mikhail S. Drenichev, Vladimir E. Oslovsky, Irina V. Kulikova, Piet Herdewijn

引用次数: 1