The Chemical Biology of Nucleic Acids

With extensive coverage of synthesis techniques and applications, this text describes chemical biology techniques which have gained significant impetus during the last five years. It focuses on the methods for obtaining modified and native nucleic acids, and their biological applications. Topics covered include: chemical synthesis of modified RNA expansion of the genetic alphabet in nucleic acids by creating new base pairs chemical biology of DNA replication: probing DNA polymerase selectivity mechanisms with modified nucleotides nucleic-acid-templated chemistry chemical biology of peptide nucleic acids (PNA) the interactions of small molecules with DNA and RNA the architectural modules of folded RNAs genesis and biological applications of locked nucleic acid (LNA) small non-coding RNA in bacteria microRNA-guided gene silencing nucleic acids based therapies innate immune recognition of nucleic acid light-responsive nucleic acids for the spatiotemporal control of biological processes DNA methylation frameworks for programming RNA devices RNA as a catalyst: The Diels-Alderase-Ribozyme evolving an understanding of RNA function by in vitro approaches the chemical biology of aptamers: synthesis and applications nucleic acids as detection tools bacterial riboswitch discovery and analysis The Chemical Biology of Nucleic Acids is an essential compendium of the synthesis of nucleic acids and their biological applications for bioorganic chemists, chemical biologists, medicinal chemists, cell biologists, and molecular biologists.

With extensive coverage of synthesis techniques and applicationsthis text describes chemical biology techniques which have gainedsignificant impetus during the last five years. It focuses on themethods for obtaining modified and native nucleic acids, and theirbiological applications. Topics covered include:* chemical synthesisof modified RNA* expansion of the genetic alphabet in nucleic acids by creatingnew base pairs* chemical biology of DNA replication: probing DNA polymeraseselectivity mechanisms with modified nucleotides* nucleic-acid-templated chemistry* chemical biology of peptide nucleic acids (PNA)* the interactions of small molecules with DNA and RNA* the architectural modules of folded RNAs* genesis and biological applications of locked nucleic acid(LNA)* small non-coding RNA in bacteria* microRNA-guided gene silencing* nucleic acids based therapies* innate immune recognition of nucleic acid* light-responsive nucleic acids for the spatiotemporal controlof biological processes* DNA methylation* frameworks for programming RNA devices* RNA as a catalyst: The Diels-Alderase-Ribozyme* evolving an understanding of RNA function by in vitroapproaches* the chemical biology of aptamers: synthesis andapplications* nucleic acids as detection tools* bacterial riboswitch discovery and analysisThe Chemical Biology of Nucleic Acids is anessential compendium of the synthesis of nucleic acids andtheir biological applications for bioorganic chemists, chemicalbiologists, medicinal chemists, cell biologists, and molecularbiologists.

Foreword viiPreface ixList of Contributors xi1 Chemical Synthesis of Modified RNA 1Claudia Höbartner and Falk Wachowius2 Expansion of the Genetic Alphabet in Nucleic Acids by Creating New Base Pairs 39Ichiro Hirao and Michiko Kimoto3 Chemical Biology of DNA Replication: Probing DNA Polymerase Selectivity Mechanisms with Modified Nucleotides 63Andreas Marx4 Nucleic Acid-templated Chemistry 73Michael Oberhuber5 Chemical Biology of Peptide Nucleic Acids (PNAs) 103Peter E. Nielsen6 The Interactions of Small Molecules with DNA and RNA 115Yun Xie, Victor K. Tam and Yitzhak Tor7 The Architectural Motifs of Folded RNAs 141Valérie Fritsch and Eric Westhof8 Genesis and Biological Applications of Locked Nucleic Acids (LNAs) 175Harleen Kaur and Souvik Maiti9 Small Non-coding RNA in Bacteria 199Sabine Brantl10 MicroRNA-guided Gene Silencing 223Gunter Meister11 Nucleic Acid-based Therapies 233Britta Hoehn and John J. Rossi12 Innate Immune Recognition of Nucleic Acids 261Stefan Bauer13 Light-responsive Nucleic Acids for the Spatiotemporal Control of Biological Processes 279Alexander Heckel and Günter Mayer14 DNA Methylation 307Albert Jeltsch and Renata Z. Jurkowska15 Frameworks for Programming RNA Devices 323Maung Nyan Win, Joe C. Liang and Christina D. Smolke16 RNA as a Catalyst: The Diels-Alderase Ribozyme 339Andres Jäschke17 Evolving an Understanding of RNA Function by In Vitro Approaches 355Qing Wang and Peter J. Unrau18 The Chemical Biology of Aptamers: Synthesis and Applications 377Günter Mayer and Bernhard Wulffen19 Nucleic Acids as Detection Tools 401Jeffrey C.F. Lam, Sergio Aguirre and Yingfu li20 Bacterial Riboswitch Discovery and Analysis 433Tyler D. Ames and Ronald R. BreakerIndex 455