Nucleic Acids

Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.

The structure, function and reactions of nucleic acids are central to molecular biology and are crucial for the understanding of complex biological processes involved. Revised and updated Nucleic Acids in Chemistry and Biology 3rd Edition discusses in detail, both the chemistry and biology of nucleic acids and brings RNA into parity with DNA. Written by leading experts, with extensive teaching experience, this new edition provides some updated and expanded coverage of nucleic acid chemistry, reactions and interactions with proteins and drugs. A brief history of the discovery of nucleic acids is followed by a molecularly based introduction to the structure and biological roles of DNA and RNA. Key chapters are devoted to the chemical synthesis of nucleosides and nucleotides, oligonucleotides and their analogues and to analytical techniques applied to nucleic acids. The text is supported by an extensive list of references, making it a definitive reference source. This authoritative book presents topics in an integrated manner and readable style. It is ideal for graduate and undergraduates students of chemistry and biochemistry, as well as new researchers to the field.

Since the discovery of the DNA double helix in 1953, nucleic acids have formed the central theme of much of contemporary molecular science. Nowhere is this more apparent than in the increasing efforts to determine the DNA sequence of the human genome and the development of new diagnostics of genetic disease. Recent sophistication of nucleic acids synthesis has been key to the establishment of the biotechnology industry and our improving knowledge of nucleic acid structures and interactions is noticeably influencing the design of novel drugs.This second and completely revised edition draws on the expertise of the same international group of authors to set the basics of the nucleic acids in the context of the expanding horizons set by modern structural biology, RNA enzymology, drug discovery and biotechnology.

Peptide nucleic acids (PNAs) have now existed for slightly more than ten years, with the interest in and applications of this pseudopeptide DNA mimic steadily increasing during the entire period. PNAs have rapidly attracted the attention of scientists from a diversity of fields ranging from (bio)organic and biophysical chemistry to prebiotic evolution, and from molecular biology to genetic diagnostics and drug development. Many of the applications take advantage of the unique properties of PNA—an uncharged pseudopeptide—that distinguish this DNA mimic from more traditional DNA analogs. Rather than trying to create a comprehensive collection of all published methods and protocols involving PNA—many of which have not yet been validated— I have decided to concentrate on select protocols that are either very well established by several groups around the world, such as PCR-clamping and in situ hybridization, or on new methods that may have broader future impact. Basic methods for PNA oligomer synthesis and analyses have also been included. I am very grateful to those friends and colleagues who have enthusiastically contributed their work, discussions, and writing, and thereby made this book possible. Peter E. Nielsen v Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix IINTRODUCTION 1 PNA Technology Peter E. Nielsen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 II CHEMISTRY 2 Solid Phase Synthesis of PNA Oligomers Frederik Beck. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 3 Synthesis of PNA-Peptide Conjugates Satish Kumar Awasthi and Peter E. Nielsen. . . . . . . . . . . . . . . . . . 43 4 Parallel Synthesis of PNA-Peptide Conjugate Libraries Satish Kumar Awasthi and Peter E. Nielsen. . . . . . . . . . . . . . . . . .

The study of nucleic acids is one of the most rapidly developing fields in modern science. The exceptionally important role of the nucleic acids as a key to the understanding of the nature of life is reflected in the enormous number of published works on the subject, including many outstanding monographs and surveys. The pathways of syn thesis and metabolism of nucleic acid,s and the many and varied biological functions of these biopolymers are examined with the utmost detail in the literature. Nearly as much attention has been paid to the macromolecular chemistry of the nucleic acids: elucidation of the size and shape of their molecules, the study of the physicochemical properties of their solutions, and the appropriate methods to be used in such research. The surveys of the chemistry of nucleic acids which have been published so far deal almost entirely with their synthesis and, in particular, with the synthetic chemistry of monomers (nucleosides and nucleotides) ; less attention has been paid to the synthesis of poly nucleotides. There is yet another highly important aspect of the chemistry of nucleic acids which is still in the formative stage, the study of the reactivity of nucleic acid macromolecules and their components. This can make an important contribution to the deter mination of the structure of these remarkable biopolymers and to the correct understanding of their biological functions.

When the first edition of this book was published in 1950, it predated the publication of the double-helical structure of DNA by three years. It is not, therefore, surprizing that nothing of the original book remains in the current edition. Indeed, such is the pace of change in the field of nucleic acids that less than 50% of material incorporated into the 1986 edition has been retained. The book aims at the advanced undergraduate and at graduates that are undertaking course work or requiring an in-depth background for their research. It also aims to provide the established scientist with a single text that permits updating across the whole field from DNA structure, replication and repair, through gene expression and its control to protein synthesis. Every chapter is accompanied by thorough referencing that enables the reader to evaluate personally the data and methodology that cannot be included in the text. In an attempt to keep this list within bounds, references are limited to about ten per page and, to accommodate the more recent literature, many of the older references have been left out in this latest edition.

Extracellular nucleic acids have recently emerged as important players in the fields of biology and the medical sciences. In the last several years, extracellular nucleic acids have been shown to be involved in not only microbial evolution as genetic elements but also to have structural roles in bacterial communities, such as biofilms. Circulating DNA and RNA have been found in human blood and expected to be useful as non-invasive markers for the diagnosis of several diseases. In addition, extracellular nucleic acids have attracted attention as active modulators of the immune system of higher organisms, including humans. This book covers nearly all of the newly developing fields related to extracellular nucleic acids, including those of basic biology, ecology and the medical sciences, and provides readers with the latest knowledge on them.

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.