Biophysical and Biochemical Aspects of Fluorescence Spectroscopy PDF
Preview Biophysical and Biochemical Aspects of Fluorescence Spectroscopy
BIOPHYSICAL AND BIOCHEMICAL ASPECTS OF FLUORESCENCE SPECTROSCOPY BIOPHYSICAL AND BIOCHEMICAL ASPECTS OF FLUORESCENCE SPECTROSCOPY Edited by T. Gregory Dewey University of Denver Denver, Colorado Springer Science+Business Media, LLC Library of Congress Catalog1ng-1n-PublicatIon Data Biophysical and biochemical aspects of fluorescence spectroscopy / edited by T. Gregory Dewey, p. cm. Includes bibliographical references and Index. 1, Fluorescence spectroscopy. 2. Biochemistry—Methodology. 3. Molecular biology—Methodology. I. Dewey, Thomas Gregory, 1952- QP519.9.F56B56 1991 574.19*285—dc20 90-25341 CIP ISBN 978-1-4757-9515-8 ISBN 978-1-4757-9513-4 (eBook) DOI 10.1007/978-1-4757-9513-4 © Springer Science+Business Media New York 1991 Originally published by Plenum Press, New York in 1991 Softcover reprint of the hardcover 1st edition 1991 All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher Contributors Barbara Baird, Department of Chemistry, Cornell University, Ithaca, New York 14853-6401 John Brumbaugh, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588 Richard A. Cardullo, Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts 01545 Richard A. Cerione, Department of Pharmacology, Cornell University, Ith aca, New York 14853-6401 T. Gregory Dewey, Department of Chemistry, University of Denver, Denver, Colorado 80208 Maurice R. Eftink, Department of Chemistry, University of Mississippi, University, Mississippi 38677 Jon Erickson, Pierre A. Fish Laboratory, Department of Pharmacology, New York State College of Veterinary Medicine, Cornell University, New York, New York 14853-6401 Paramjit K. GharyaI, Department of Biochemistry, Michigan State Univer sity, East Lansing, Michigan 48824 Byron Goldstein, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87544 Dan Grone, Li-Cor, Inc., Lincoln, Nebraska 68504 Theodore L. Hazlett, Department of Biochemistry and Biophysics, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96822 David Holowka, Department of Chemistry, Cornell University, Ithaca, New York 14853 David M. Jameson, Department of Biochemistry and Biophysics, John A. v vi Contributors Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96822 Lian-Wei Jiang, Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824 Lyle Middendorf, Li-Cor, Inc., Lincoln, Nebraska 68504 Robert M. Mungovan, Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts 01545 Matthew Petersheim, Department of Chemistry, Seton Hall University, South Orange, New Jersey 07079 William J. Phillips, Department of Pharmacology, Cornell University, Ith aca, New York 14853-6401 Richard Posner, Department of Chemistry, Cornell University, Ithaca, New York 14853-6401 Jerry Ruth, Molecular Biosystems, Inc., San Diego, California 92121 Melvin Schindler, Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824 David E. Wolf, Worcester Foundation for Experimental Biology, Shrews bury, Massachusetts 01545 Preface Fluorescence spectroscopy has traditionally found wide application in bio chemistry and cell biology. Since there are relatively few naturally occurring fluorescent biomolecules, fluorescence spectroscopy offers a combination of great specificity and sensitivity. Historically, these features have been ex ploited with great success utilizing both intrinsic and extrinsic probes. Re cent applications have built upon these traditional strengths and have re sulted in the development of new instrumental techniques, novel and convenient fluorescent probes, and a deeper, theoretical understanding of fundamental processes. Frequently, fluorescence techniques are tailored to attack a specific biological problem. These new methods in turn produce new physical situations and phenomena which are often of interest to the physical chemist. Thus, progress in one area stimulates renewed interest in other areas. The goal of this book is to provide detailed monographs on the use of fluorescence to investigate problems at the forefront of biochemistry and cell biology. This book is not meant to be a comprehensive survey but rather to highlight areas of recent developments. It is designed to be readable to the novice and yet provide sufficient detail for the expert to keep abreast of recent developments. The book is organized so that it proceeds from simple biochemical sys tems to more complex cell biological ones. Chapter I on fluorescence quenching of biological structures is a good introductory chapter. It intro duces a number of elementary concepts and discusses applications to pro teins and biomembranes. This chapter reveals the relative ease of obtaining structural dynamic information using fluorescence quenching. The role of divalent cations in biological systems has attracted considerable recent atten tion. Chapter 2 presents the properties of fluorescent analogues to divalent vii viii Preface cations, the lanthanides. It discusses in detail how water coordination and cation binding site heterogeneity can be determined in biological systems. The controversial use of lanthanides for obtaining distance information by fluorescence energy transfer is also critically reviewed. In Chapter 3 fluores cence applications to a new technology, on-line, real time DNA sequencing -is discussed. The synthesis and sequencing reactions of fluorescently la beled nucleic acid primers are examined. The development of real time sequencing capabilities with multiple fluorescent primers offers an exciting and potentially powerful alternative to conventional techniques. Chapter 4 provides an excellent introduction to the use of fluorescence anisotropy for the study of macromolecular motion. A description of both time-resolved and modulation instrumentation and data analysis is presented. Applica tions to molecular motions oftRNA and elongation factor Tu are discussed. Chapter 5 is another good general chapter that demonstrates application of a variety of fluorescence techniques to increasingly complex systems. It ex plores the use of fluorescence energy transfer and fluorescence quenching to study receptor-G protein interactions. The focus is more on the system and this chapter demonstrates how both intrinsic and extrinsic fluorescent probes can be utilized to attack biochemical problems. Chapter 6 is along similar lines as Chapter 5. It concentrates on antibody-receptor interactions. Again, fluorescence spectroscopy is the tool used for characterizing protein protein interactions. The kinetics and aggregation of receptors are studied with the goal ofd eveloping quantitative models. The biological membrane is a crucial component in these more complicated systems and fluorescence applications to membrane systems are covered in more detail in Chapter 7. This chapter describes the use of fluorescence energy transfer to obtain struc tural and dynamic information on proteins in artificial membrane systems. Chapters 8 and 9 proceed along this line to cellular systems. Chapter 8 dis cusses fluorescence energy transfer and photobleaching on cell surfaces. The energy transfer experiments represent a new application of video imaging of cell surfaces. A significant portion of this chapter deals with the technology of fluorescence video imaging of cells. Chapter 9 is a good background chapter on fluorescence photobleaching. It also discusses several cell biologi cal problems involving membrane organization and dynamics. Experimen tal work on a variety of membrane transport processes is examined. There are several themes which loosely run through this book. One is the similarity of techniques used to attack biological problems. The chemis try of fluorescent labeling has common features in a diversity of systems. Fluorescence quenching, energy transfer, and anisotropy appear in different contexts as techniques for obtaining structural and dynamic information. Although in many cases complex biochemical systems are studied, a signifi- Preface ix cant quantitative rigor is involved. This persists from data analysis to theoret ical models. These common features assist interactions between investiga tors who work on very different systems. It is hoped that this collection of monographs reveals the excitement and the diversity of skills and ap proaches used in current research. T. Gregory Dewey Denver Contents Chapter 1 Fluorescence Quenching Reactions: Probing Biological Macromolecular Structures Maurice R. Eftink 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2. Basic Concepts ................................................. 2 2.1. The Stern-Volmer Equation ............................... 2 2.2. Heterogeneous Emission ................................... 7 2.3. Partitioning among Subphases ............................. 8 3. Experimental Details ........................................... 9 4. Data Analysis ................................................. 16 5. Experimental Strategies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 5.1. Fluorescence Lifetime Measurements ..................... 21 5.2. Variation of Quencher Size, Charge, and Polarity.......... 24 5.3. Variation ofIonic Strength and pH ....................... 25 5.4. Variation of Temperature, Pressure, and Viscosity......... 26 5.5. Variation of the State of the Biomacromolecule ........... 28 5.6. Variation of the Fluorophore ............................. 28 5.7. Use of Quencher-Lipid Molecules......................... 29 6. Examples of Topographical Solute Quenching Studies.......... 29 7. Conclusion.................................................... 37 8. References .................................................... 39 xi
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