Non-Natural Nucleic Acids: Methods and Protocols
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This volume provides relevant synthetic strategies, incorporation, and applications of non-natural nucleic acids. Chapters detail monomer synthesis, oligomer synthesis/construction, and applications allowing researchers to explore and determine which methodology or methodologies are relevant to their needs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Non-Natural Nucleic Acids: Methods and Protocols aims to serve as a guide for researchers exploring their own inquiries and to provide a springboard for new endeavors. Front Matter ....Pages i-xi Synthesis and Enzymatic Characterization of Sugar-Modified Nucleoside Triphosphate Analogs (Stella Diafa, Damien Evéquoz, Christian J. Leumann, Marcel Hollenstein)....Pages 1-13 Synthesis of Site-Specific Crown Ether Adducts to DNA Abasic Sites: 8-Oxo-7,8-Dihydro-2′-Deoxyguanosine and 2′-Deoxycytidine (Na An, Aaron M. Fleming, Nicole C. Rosecrans, Yi Liao, Cynthia J. Burrows)....Pages 15-25 Synthesis of a Fluorescent Cytidine TNA Triphosphate Analogue (Hui Mei, John Chaput)....Pages 27-37 Synthesis of Base-Modified dNTPs Through Cross-Coupling Reactions and Their Polymerase Incorporation to DNA (Petra Ménová, Hana Cahová, Milan Vrábel, Michal Hocek)....Pages 39-57 2′-C,4′-C-Ethyleneoxy-Bridged 2′-Deoxyribonucleic Acids (EoDNAs) with Thymine Nucleobases: Synthesis, Duplex-Forming Ability, and Enzymatic Stability (Takashi Osawa, Satoshi Obika, Yoshiyuki Hari)....Pages 59-89 Synthesis Protocols for Simple Uncharged Glycol Carbamate Nucleic Acids (Tanaya Bose, Vaijayanti A. Kumar)....Pages 91-106 Synthesis of Nucleobase-Functionalized Morpholino Monomers (Bappaditya Nandi, Sankha Pattanayak, Sibasish Paul, Jayanta Kundu, Surajit Sinha)....Pages 107-130 Synthesis and Application of LKγT Peptide Nucleic Acids (Nathaniel Shank, Kara M. George Rosenker, Ethan A. Englund, Andrew V. Dix, Elizabeth E. Rastede, Daniel H. Appella)....Pages 131-145 Aminoglycoside Functionalization as a Tool for Targeting Nucleic Acids (Derrick Watkins, Krishnagopal Maiti, Dev P. Arya)....Pages 147-162 Preparation and Purification of Oligodeoxynucleotide Duplexes Containing a Site-Specific, Reduced, Chemically Stable Covalent Interstrand Cross-Link Between a Guanine Residue and an Abasic Site (Maryam Imani Nejad, Xu Guo, Kurt Housh, Christopher Nel, Zhiyu Yang, Nathan E. Price et al.)....Pages 163-175 Copper-Catalyzed Alkyne-Azide Cycloaddition on the Solid Phase for the Preparation of Fully Click-Modified Nucleic Acids (Malte Rosenthal, Franziska Pfeiffer, Günter Mayer)....Pages 177-183 Labeling Peptide Nucleic Acids with Indium-111 (Igor G. Panyutin)....Pages 185-191 Site-Specific Labeling of DNA via PCR with an Expanded Genetic Alphabet (Michael P. Ledbetter, Denis A. Malyshev, Floyd E. Romesberg)....Pages 193-212 Flexible Nucleic Acids (FNAs) as Informational Molecules: Enzymatic Polymerization of fNTPs on DNA Templates and Nonenzymatic Oligomerization of RNA on FNA Templates (Maryline Chemama, Christopher Switzer)....Pages 213-236 Artificial Nucleosides as Diagnostic Probes to Measure Translesion DNA Synthesis (Jung-Suk Choi, Anthony Berdis)....Pages 237-249 FRET Assay for Ligands Targeting the Bacterial A-Site RNA (Renatus W. Sinkeldam, Yitzhak Tor)....Pages 251-260 The Use of Serinol Nucleic Acids as Ultrasensitive Molecular Beacons (Keiji Murayama, Hiromu Kashida, Hiroyuki Asanuma)....Pages 261-279 Oligonucleotide Primers with G8AE-Clamp Modifications for RT-qPCR Detection of the Low-Copy dsRNA (Timofei S. Zatsepin, Anna M. Varizhuk, Vladimir G. Dedkov, German A. Shipulin, Andrey V. Aralov)....Pages 281-297 Determining Steady-State Kinetics of DNA Polymerase Nucleotide Incorporation (Hailey L. Gahlon, Shana J. Sturla)....Pages 299-311 Back Matter ....Pages 313-315
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