Handbook of Biochemistry

Section B Nucleic Acids, Volume I

Gerald D Fasman

• Publisher: CRC Press
• Year: 2019
• Print ISBN: 9781315893280
• eBook ISBN: 9781351089289
• Topic: Medicine
• Subtopic: Biochemistry in Medicine

This volume contains information on the nucleotide composition of bacterial DNA. Eukaryotic protists, etc.; Nearest neighbour frequencies in DNA; repeated and unique sequences in eukaryotes; nucleic acid sequences in bacteriophage, chloroplasts, mitochondria, kinetoplasts, satellites and TRNA. Information on the physical properties of RNA, atomic coordinates of DNA-DNA. Also included in this volume is information on enzymes involved in nucleic acid function.

PREFACE TO NUCLEIC ACIDS, VOLUME 1

The section of the Handbook of Biochemistry and Molecular Biology on Nucleic Acids is divided into two volumes. The first volume contains information relating to purines, pyrimidines, nucleosides, nucleotides, oligonucleotides, polynucleotides, and their derivatives. Both ribo and deoxyribo compounds are listed, starting from their respective monomeric units and encompassing all materials up to and including RNA and DNA.

The following list is representative of the data for the above materials contained herein: Physical constants, spectral constants, ultraviolet absorption characteristics, optical properties (optical rotatory and circular dichroism), osmotic coefficients, proton chemical shifts, raman spectral bands, temperature melting profiles, and infrared spectra.

The second volume will contain the remaining material similar to Volume 1 and material more relative to genetic and biological aspects, such as enzymes involved in nucleic acid function, protein synthesis, linkage maps, etc.

Although the data, for which the editor alone is responsible, is far from complete, it is hoped these volumes will be of assistance to those working in the field of biochemistry and molecular biology.

Gerald D. Fasman
Editor
September 1975

THE EDITOR

Gerald D. Fasman, Ph.D., is the Rosenfield Professor of Biochemistry, Graduate Department of Chemistry, Brandeis University, Waltham, Massachusetts.

Dr. Fasman graduated from the University of Alberta in 1948 with a B.S. Honors Degree in Chemistry, and he received his Ph.D. in Organic Chemistry in 1952 from the California Institute of Technology, Pasadena, California. Dr. Fasman did postdoctoral studies at Cambridge University, England, Eidg. Technische Hochschule, Zurich, Switzerland, and the Weizmann Institute of Science, Rehovoth, Israel. Prior to moving to Brandeis University, he spent several years at the Children’s Cancer Research Foundation at the Harvard Medical School. He has been an Established Investigator of the American Heart Association, a National Science Foundation Senior Postdoctoral Fellow in Japan, and recently was a John Simon Guggenheim Fellow.

Dr. Fasman is a member of the American Chemical Society, a Fellow of the American Association for the Advancement of Science, Sigma Xi, The Biophysical Society, American Society of Biological Chemists, The Chemical Society (London), the New York Academy of Science, and a Fellow of the American Institute of Chemists. He has published 180 research papers.

The Editor and CRC Press, Inc. would like to dedicate this third edition to the memory of Eva K. and Herbert A. Sober. Their pioneering work on the development of the Handbook is acknowledged with sincere appreciation.

TABLE OF CONTENTS

NOMENCLATURE

Biochemical Nomenclature

IUPAC Tentative Rules for the Nomenclature of Organic Chemistry Section E. Fundamental Stereochemistry

Abbreviations for Pyrimidine Photoproducts

Nomenclature of Labeled Compounds

The Citation of Bibliographic References in Biochemical Journals, Recommendations (1971)

PURINES, PYRIMIDINES, NUCLEOTIDES AND OLIGONUCLEOTIDES

Purines, Pyrimidines, Nucleosides, and Nucleotides: Physical Constants and Spectral Properties

Natural Occurrence of the Modified Nucleosides

Purine, Pyrimidine, Pyridine, and Imidazole Derivatives Excreted in Human Urine

Nucleoside Antibiotics: Physico-chemical Constants, Spectral, Chemotherapeutic, and Biological Properties

Controlled Partial Hydrolysis of RNA

Spectrophotometric Constants of Ribonucleotides

UV Spectral Characteristics and Acidic Dissociation Constants of 280 Alkyl Bases, Nucleosides, and Nucleotides

Ultraviolet Absorbance of Oligonucleotides containing 2’-0-Methylpentose Residues

Optical Rotatory Dispersion Parameters of Oligonucleotides of RNA

Circular Dichroism Parameters of 2’-0-Methylated Dinucleoside Monophosphates

Vapor Phase Osmometry Coefficients on Nucleic Acid Bases and Nucleosides

Proton Magnetic Resonance Data on Mononucleotides, Oligonucleotides, and Polynucleotides in D₂O

Raman Spectral Bands of Nucleic Acids and their Components

NUCLEIC ACIDS AND POLYNUCLEOTIDES

Viral DNA Molecules

Some Properties of Viral Deoxyribonucleic Acids – Buoyant Densities, Melting Temperatures, and GC Content

Buoyant Densities of Nucleic Acids and Polynucleotides

Melting Temperatures T_m (°C) of Synthetic Polynucleotides

Optical Properties of Nucleic Acids, Absorption, and Circular Dichroism Spectra

Use of Tables in Calculation of Absorption, Optical Rotatory Dispersion, and Circular Dichroism of Polyribonucleotides

Infrared Properties of Polynucleotides

INDEX

Nomenclature

Biochemical Nomenclature

This synopsis of the recommendations of the IUPAC-IUB Commission on Biochemical Nomenclature (CBN) was prepared by Waldo E. Cohn, Director, NAS-NRC Office of Biochemical Nomenclature (OBN, located at Biology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830), from whom reprints of the CBN publications listed below and on which the synopsis is based are available.

The synopsis is divided into three sections: Abbreviations, symbols, and trivial names. Each section contains material drawn from the documents (Al to CI, inclusive) listed below, which deal with the subjects named.

Additions consonant with the CBN Recommendations have been made by OBN throughout the synopsis.

Rules and Recommendations Affecting Biochemical Nomenclature and Places of Publication (as of February 1975)

1. IUPAC-IUB Commission on Biochemical Nomenclature
   • A1. Abbreviations and Symbols [General; Section 5 replaced by A6)
   • A2. Abbreviated Designation of Amino-acid Derivatives and Peptides (1965) [Revised 1971; Expands Section 2 of Al]
   • A3. Synthetic Modifications of Natural Peptides (1966) [Revised 1972]
   • A4. Synthetic Polypeptides (Polymerized Amino Acids) (1967) [Revised 1971]
   • A5. A One-letter Notation for Amino-acid Sequences (1968)
   • A6. Nucleic Acids, Polynucleotides, and their Constituents (1970)
   • B1. (Nomenclature of Vitamins, Coenzymes, and Related Compounds)
     1. Miscellaneous [A, B's, C, D's, tocols, niacins; see B2 and B3]
     2. Quinones with Isoprenoid Side-chains: E, K, Q [Revised 1973]
     3. Folic Acid and Related Compounds
     4. Corrinoids: B-12's...

Table of contents

• Cover
• Half Title
• Title Page
• Copyright Page
• Advisory Board
• Contributors
• Preface
• Preface to Nucleic Acids, Volume 1
• The Editor
• Dedication
• Table of Contents
• NOMENCLATURE
• PURINES, PYRIMIDINES, NUCLEOTIDES AND OLIGONUCLEOTIDES
• NUCLEIC ACIDS AND POLYNUCLEOTIDES
• INDEX