Photochemistry and Photobiology of Nucleic Acids. Biology

434 Pages·1976·5.54 MB·English

by  Shih Yi Wang (Eds.)

Contributors
Peter A. Cerutti
W. E. Cohn
C. O. Doudney
Milton P. Gordon
Helga Harm
Chaog-wei Huang
Jakob Hurter
John Jagger
N. J. Leonard
Μ. H. Patrick
R. O. Rahn
Kendric C. Smith
S. Y. Wang
Photochemistry and
Photobiology of
Nucleic Acids
Volume II
Biology
EDITED BY
Shih Yi Wang
Department of Biochemistry
School of Hygiene and Public Health
The Johns Hopkins University
Baltimore, Maryland
with Michael H. Patrick as coordinator
ACADEMIC PRESS New York San Francisco London 1976
A Subsidiary of Harcourt Brace Jovanovich, Publishers
COPYRIGHT © 1976, BY ACADEMIC PRESS, INC.
ALL RIGHTS RESERVED.
NO PART OF THIS PUBLICATION MAY BE REPRODUCED OR
TRANSMITTED IN ANY FORM OR BY ANY MEANS, ELECTRONIC
OR MECHANICAL, INCLUDING PHOTOCOPY, RECORDING, OR ANY
INFORMATION STORAGE AND RETRIEVAL SYSTEM, WITHOUT
PERMISSION IN WRITING FROM THE PUBLISHER.
ACADEMIC PRESS, INC.
Ill Fifth Avenue, New York, New York 10003
United Kingdom Edition published by
ACADEMIC PRESS, INC. (LONDON) LTD.
24/28 Oval Road, London NW1
Library of Congress Cataloging in Publication Data
Main entry under title:
Photochemistry and photobiology of nucleic acids.
Includes bibliographies and index.
CONTENTS: -v. 2. Photobiology.
1. Nucleic acids. 2. Photochemistry. 3. Photo­
biology. I. Wang, Shih Yi, (date)
QD433.P48 547'596 75-26528
ISBN 0-12-734602-3
PRINTED IN THE UNITED STATES OF AMERICA
List of Contributors
Numbers in parentheses indicate the pages on which the authors' con­
tributions begin.
Peter A. Cerutti (375), Department of Biochemistry, University of
Florida, Gainesville, Florida
W. E. Cohn (403), NAS-NRC Office of Biochemical Nomenclature,
Biology Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee
C. O. Doudney (309),* Department of Genetics, Albert Einstein Medical
Center, Philadelphia, Pennsylvania
Milton P. Gordon (265), Department of Biochemistry, University of
Washington, Seattle, Washington
Helga Harm (219), Institute for Molecular Biology, University of
Texas at Dallas, Richardson, Texas
Chaog-wei Huang (265), Department of Biochemistry, University of
Washington, Seattle, Washington
Jacob Hurter (265),t Department of Biochemistry, University of
Washington, Seattle, Washington
John Jagger (147), Department of Molecular Biology, University of
Texas at Dallas, Richardson, Texas
N. J. Leonard (403), Department of Chemistry, University of Illinois,
Urbana, Illinois
* Present address: Division of Laboratories and Research, New York State Department
of Health, New Scotland Avenue, Albany, New York 12201
+ Present address: Swiss Federal Research Station, CH-8820 Wadenswil, Switzerland
ix
χ LIST OF CONTRIBUTORS
Μ. Η. Patrick (1, 35, 97), Institute for Molecular Biology, University of
Texas at Dallas, Richardson, Texas
R. O. Rahn (35, 97), Biology Division, Oak Ridge National Laboratories,
Oak Ridge, Tennessee
Kendric C. Smith (187), Department of Radiology, Stanford Uni­
versity School of Medicine, Stanford, California
S. Y. Wang (403), Department of Biochemistry, School of Hygiene and
Public Health, The Johns Hopkins University, Baltimore, Mary­
land
Preface
The prospect of understanding living processes through physical
and chemical principles has attracted many physical scientists to the
study of molecular biology. Since the mid 1930's, their enthusiasm
plus that of biologists has brought about unparalleled advances in
many areas of biology. One of the areas which requires the actual inter­
action of physicists, chemists, and biologists is photobiology. It is this
interaction which is particularly fascinating and has drawn many to
the study of photobiology. Such a trend proved to be fruitful in the
study of photochemistry of nucleic acid components, and early work
led to the isolation and characterization of ultraviolet photoproducts
of pyrimidines. This discovery, in turn, touched off a high level of
activity in the study of photobiology of nucleic acids at the molecular
level. Current activity in this area is unprecedented in the history of
photobiological studies. This intensive and concerted effort has re­
sulted in the recognition not only of processes of repair of and of pro­
tection against irradiation damage in biological systems but also of the
possible relevancy of pyrimidine photoproducts to mutagenesis and
carcinogenesis.
This two-volume treatise provides a judicious review of these excit­
ing developments with up-to-date information as well as the necessary
background knowledge. The chapters, each a self-contained entity, are
concise and authoritive reviews by a group of researchers who are
active in their respective areas. Since this is a vigorous field of study,
the range of statements necessarily extends from those with a high
probability of continuing certainty to those that are speculative but
potentially of heuristic value. This should convey to our readers the
explorative attitude of the investigators and the excitement inherent in
this research. While the orientation of each chapter naturally reflects
xi
xii PREFACE
the interests and viewpoint of the author, there has been a genuine
effort to present a critical treatment of the existing data.
Volume I is concerned with the UV-induced physical and chemical
alterations in nucleic acid components including pyrimidines, purines,
their nucleosides and nucleotides, and related compounds. In addi­
tion, chapters on mass and nuclear magnetic resonance spectrometry
and crystal and molecular structural determinations by x-ray diffrac­
tion are included. Together with the pertinent examples, a brief discus­
sion of the theory and techniques is also presented in each chapter.
This should be of considerable help to those who, although not per­
sonally involved in the interpretation of data, may wish to understand
and possibly evaluate reported findings. Also, the close relationship
between the chemical effects of UV light and x- or γ-radiation prompted
the inclusion of a chapter on radiation chemistry for the purpose of
comparison.
Volume II is concerned with the biological effects due to stable UV-
induced alterations in critical cellular macromolecules including cell
death, growth delay, mutagenesis, and carcinogenesis. The fact that
the problem has been most successfully pursued by assuming DNA to
be the macromolecule most relevant to cell pathology is reflected in
most of the chapters. It is also necessary to consider the photochemical
and photobiological properties of RNA's which are also essential in
cellular functions. Although knowledge about protein and amino acid
photochemistry is less advanced than that of nucleic acids, a chapter
dealing with the UV-induced cross-linkings of proteins with nucleic
acids is appropriate. This knowledge may be required for a full under­
standing of the mode of action of UV on cells, since it is improbable
that biological effects can be explained solely in terms of damage to
nucleic acids. Later chapters delve into the mechanisms that provide
some protection against and are capable of repairing damage caused by
UV photons and by ionizing radiation (also chemical mutagens) in
organisms ranging from viruses to mammalian cells. These repair
processes which were initially of concern only to photobiologists have
gained the interest of investigators in other areas of molecular biology.
Apparently, repair processes play a role in monitoring and preserving
the structural integrity of DNA during physiological processes such as
replication and transcription. Because of this widespread interest,
research of these repair processes has mushroomed in recent years.
Although the study of photoreactivation may have been effectively
covered in a single chapter, such a treatment of the vast existing
literature on "dark repair" would have been insufficient. Additionally,
knowledge concerning these complex processes is in a state of flux.
PREFACE xiii
For these reasons such a review has not been included in these vol­
umes.
This treatise should serve as an authoritative and important refer­
ence work for researchers active in the study of photochemistry and
photobiology in nucleic acids as well as for advanced undergraduate
and graduate students interested in this field. Since this is an inter­
disciplinary area, an attempt has been made to direct our writings to
an audience which includes physicists, chemists, biologists, and
physicians.
An attempt was made to further a balanced viewpoint by requesting
two or more scholars, active in the respective areas, to review each
chapter. I wish to thank all of these reviewers, some of whom are
contributors, for their most helpful criticisms, comments, and sugges­
tions. These reviewers include the late Ruth F. Hill (York University);
A. A. Lamola (Bell Laboratory); E. Fahr (Universität Würzburg); J. Ε.
Cleaver (Imperial Cancer Research Fund Laboratory); M. W. Logue
(University of Maryland Baltimore County); J. R. Williams (Temple
University); B. A. Bridges (Medical Research Council); J. F. Ward (Uni­
versity of California, Los Angeles); W. A. Summers (University of
Oklahoma); H. Werbin, W. Harm, C. S. Rupert (The University of
Texas at Dallas); L. Brand, T. Merz, J. L. Alderfer, R. M. Herriott, P. C.
Huang, J. Scocca (The Johns Hopkins University); and, in particular,
William Hauswirth who read and commented on major portions of
the text.
Finally, I wish to thank my colleagues in this endeavor. Particular
gratitude goes to Drs. John Jagger and Michael H. Patrick for discus­
sions on the organization of Volume II for which Dr. Patrick has
served as coordinator; to Elizabeth Hopkins Roth, Patricia Whiting
Linton, and Jane Entwisle Shipley for their editorial assistance; to
Sally Vasek who dealt effectively with the typing and illustrations of
all of the edited manuscripts; and to the staff of Academic Press for
their cooperation and efficient processing of this publication.
Shih Yi Wang
Contents of Volume I
Introductory Concepts for Photochemistry of Nucleic Acids
Shih Yi Wang
Excited States of the Nucleic Acids, Bases, Mononucleosides, and
Mononucleotides
Malcolm Daniels
Excited States of the Nucleic Acids, Polymeric Forms
William W. Hauswirth and Malcolm Daniels
Pyrimidine Photohydrates
Gordon J. Fisher and Η. E. Johns
Photodimerization of Pyrimidine Monomers
Gordon /. Fisher and Η. E. Johns
Pyrimidine Bimolecular Photoproducts
Shih Yi Wang
Photoproducts of Purines
Dov Elad
Aggregate Formation, Excited State Interactions, and Photochemical Reactions
in Frozen Aqueous Solutions of Nucleic Acid Constituents
Therese Montenay-Garestier, Michel Charlier, and Claude Helene
Analysis by Mass Spectrometer of the Photoproducts of Nucleic Acid Bases
Catherine Fenseiau
Nuclear Magnetic Resonance of Photoproducts
D. P. Hollis
Crystal and Molecular Structure of Photoproducts from Nucleic Acids
Isabella L. Karle
The Radiation Chemistry of Pyrimidines, Purines, and Related Substances
G. Scholes
xv
1
• Physical and Chemical
JL Properties of DNA
Μ. Η. Patrick
A. introduction 1
Β. Primary Structure 2
1. General Properties 2
2. Stabilizing Forces 4
C. Secondary Structure 6
1. Three-Dimensional Configuration 6
2. Properties of DNA in Vivo. 10
3. Properties of DNA in Vitro 13
4. Denaturation 17
D. Absorption of UV Light by DNA 22
1. Hypochromicity 22
2. Factors Influencing Absorption 26
3. Excited States and Energy Transfer in DNA 27
References 32
A. Introduction
At the foundation of molecular genetics is the fact that the chemical
properties of the nucleotide monomers govern the specific association
of the Pur and Pyr bases in DNA; this is the basis for storage, transmis­
sion, and expression of genetic information. Thus, the specific com­
plementarity of the hydrogen-bonding geometry among the four bases
determines the base sequence of daughter DNA upon replication, and
the genetic information expressed in this base sequence governs the
process of protein biosynthesis via messenger RNA.
Although alteration of any of the bases is obviously a potential
cause of molecular pathology, the actual photochemical changes
which occur in DNA can depend more on the properties manifested
by its secondary structure. To see this more clearly, consider that
l