Nucleic Acids: Structures, Properties, and Function. By Victor A. Bloomfield, Donald M. Crothers, and Ignacio Tinoco, Jr.

Nucleic Acids: Structures, Properties, and Function. By Victor A. Bloomfield, Donald M. Crothers, and Ignacio Tinoco, Jr. University Science Books: Sausalito, CA; 2000. Clothbound, 800 pp, $88.00, ISBN 0-935702-49-0.

Reviewed by, Jeffry D. Madura, Duquesne University, madura@duq.edu

Nucleic Acids: Structure, Properties, and Functions is an updated and expanded version of the successful 1974 book The Physical Chemistry of Nucleic Acids by the same authors. This newest version is a welcome addition to the rapidly changing and growing field of nucleic acids. A brief review of the book’s 14 chapters follows.

Chapter one consists of a brief overview of the biological roles of the nucleic acids and contains an outline of the book. Also included in this chapter are discussions of how nucleic acids are obtained for physical study, the nucleic acid periodical literature (including a list of books and monographs), and a section on computer analysis of sequences and structures.

The next seven chapters examine the properties of the nucleic acids, mainly at the atomic and molecular level. Chapter two covers the physical and chemical properties of monomeric building blocks of nucleic acid structure. Chapter three proceeds with a presentation of the chemical and photochemical reactivities of nucleic acids and their importance in structural determination and mutagenesis. The next three chapters describe how X-ray diffraction, and NMR, electronic, and vibrational spectroscopy are used to study the structure and dynamics of nucleic acids. In these chapters the reader is given the basic principles and results for each method. The X-ray chapter points out the need for fiber diffraction data to delineate helical parameters for long sequences that cannot be crystallized. The chapter concludes with results on nucleic acids complexed with proteins, metal ions, water, and drugs.

The chapter covering NMR describes how this technique has enhanced our understanding of the structure of mononucleotides in solution and how NMR is being used to determine the three-dimensional structure of various RNA molecules. The optical spectroscopy chapter illustrates how methods such as circular dichroism, infrared, and Raman spectroscopy are providing critical information on nucleic acid backbone and base geometry, as well as the use of these methods to give insight into the conformation of DNA inside viruses.

Chapter seven describes various computational methods currently used to provide a detailed model of the structural, energetic, and reactive properties of nucleic acids and their complexes. By contrast, chapter eight deals with nucleic acid conformational transitions from thermodynamic and kinetic points of view. In it, the various interactions that lead to the formation of helices are discussed. There is also a brief discussion of the prediction of secondary and tertiary structure of nucleic acids. Chapter nine surveys the major experimental methods used to characterize the size and shape of nucleic acids, including models of molecular structure, diffusion, rotational dynamics, scattering, viscosity, and frictional coefficients for model shapes. These are important in the interpretation of data from electrophoresis, sedimentation, dynamic light scattering, and microscopy experiments.

Chapter ten focuses on supercoiled DNA. Much of the chapter discusses the geometry and topology of DNA supercoiling with some consideration of the experimental measurement of the linking difference. The next three chapters cover the noncovalent interactions between nucleic acids and other types of molecules that affect stability or regulation function.

Chapter eleven introduces the interactions of nucleic acids with water and ions. In this chapter, topics such as hydration, polyelectrolyte behavior, hydration in ionic solutions, specific binding of metal ions, and mixed aqueous–nonaqueous solvents are presented. I found the section on metal binding to be somewhat weak, considering the amount of work being done in this area.

The interaction and reaction of nucleic acids with drugs is the topic of chapter twelve. Here the authors present both theoretical descriptions and experimental studies of binding equilibria. One section in this chapter covers natural products that react covalently with DNA. Chapter thirteen covers protein–nucleic acid interactions and is by far the largest chapter in the book. Nucleic acid–protein complexes stretch the limits of biophysical methods; however, as the authors show, these experimental methods, coupled with computer analysis characterizing binding domains, can provide a remarkable insight. The final chapter is a discussion on the higher-order structures and mechanisms in the packaging of DNA in viruses and chromatin.

Four chapters in this book are contributions from John E. Hearst (“Chemical and Enzymatic Methods”), David E. Wemmer (“Structure and Dynamics by NMR”), Peter A. Kollman (“Theoretical Methods”), and Douglas H. Turner (“Conformational Changes”). Overall this is an excellent introduction and review of the structure, properties and function of nucleic acids. The level of detail in this book is sufficient for graduate and upper-level undergraduate students to begin to explore the area of nucleic acids. The references at the end of each chapter, which are both up to date and numerous (typically more than one hundred per chapter), encourage the interested reader to pursue topics in greater depth.