Drug-DNA Interaction Protocols / Edition 2

by Keith R. Fox

Overview

DNA has been known to be the cellular target for many cytotoxic anticancer agents for several decades. The knowledge of its structure in atomic detail and the ease with which DNA fragments (both synthetic oligonucleotides and natural sequences) can be prepared and manipulated has aided the design of compounds that bind to it with improved sel- tivity. On the basis of this information, new generations of sequence reading compounds (including triplex forming oligonucleotides and minor groove binding ligands) have been prepared, which have the potential for targeting specifc DNA sequences as anti-gene agents. Within the last 10 years, it has also become apparent that the familiar DNA duplex is not the only structure that can be targeted by DNA-binding ligands and there has been increased interest in triplex and quadruplex structures as drug targets, as well as protein- DNA complexes, such as those with nucleosomes or topoisomerases. Each of these advances has required the availability and development of an arsenal of techniques for probing the interactions in both qualitative and quantitative terms. This v- ume of Methods in Molecular Biology brings together several techniques that are currently useful for examining these interactions. Some of these are updates on ones that were included in the earlier volume (Methods in Molecular Biology 90), published 12 years ago, while others are new.

Product Details

ISBN-13:	9781603274173
Publisher:	Springer-Verlag New York, LLC
Publication date:	12/17/2009
Series:	Methods in Molecular Biology , #613
Edition description:	2nd ed. 2010
Pages:	311
Product dimensions:	7.20(w) x 10.10(h) x 1.10(d)

About the Author

Fox, Keith R. (Univ of Southampton)

The contributors represent the specialties of biochemistry and molecular biology, anatomy, chemistry, pharmacology, and oncology. Most are from universities in the U.S., the U.K., Canada, and Australia. Institutions prominently represented include the Univ of Southampton, Syracuse Univ, Univ of Saskatchewan, and La Trobe Univ.

Table of Contents

preface v

Contributors ix

1 Quantitative Analysis of Small Molecule-Nucleic Acid Interactions with a Biosensor Surface and Surface Plasmon Resonance Detection Yang Liu W. David Wilson 1

2 Thermal Melting Studies of Ligand DNA Interactions Aurore Gu?din Laurent Lacroix Jean-Louis Mergny 25

3 Circular and Linear Dichroism of Drug-DNA Systems Alison Rodger 37

4 Drug Binding to DNA-RNA Hybrid Structures Richard T. Wheelhouse Jonathan B. Chaires 55

5 Quantification of Binding Data Using Capillary Electrophoresis Fitsumbirhan Araya Graham G. Skellern Roger D. Waigh 71

6 Determination of Equilibrium Association Constants of Ligand-DNA Complexes by Electrospray Mass Spectrometry Val?rie Gabelica 89

7 Detection of Adriamycin-DNA Adducts by Accelerator Mass Spectrometry Kate Coldwell Suzanne M. Cutts Ted J. Ognibene Paul T. Henderson Don R. Phillips 103

8 Molecular Modelling Methods to Quantitate Drug-DNA Interactions Hao Wang Charles A. Laughton 119

9 Application of Anomalous Diffraction Methods to the Study of DNA and DNA-Complexes Derrick Watkins Tinoush Moulaei Seiji Komeda Loren Dean Williams 133

10 DNase I Footprinting Antonia S. Cardew Keith R. Fox 153

11 Methods to Characterize the Effect of DNA-Modifying Compounds on Nucleosomal DNA Vidya Subramanian Robert M. Williams Dale L. Boger Karolin Luger 173

12 REPSA: Combinatorial Approach for Identifying Preferred Drug-DNA Binding Sequences Michael W. Van Dyke 193

13 In vitro Transcription Assay for Resolution of Drug-DNA Interactions at Defined DNA Sequences Benny J. Evison Don R. Phillips Suzanne M. Cutts 207

14 In vitro Footprinting of Promoter Regions Within Supercoiled Plasmid DNA Daekyu Sun 223

15 Topoisomerase I-Mediated DNA Relaxation as a Tool to Study Intercalation of Small Molecules into Supercoiled DNA Paul Peixota Christian Bailly Marie-H?l?ne David-Cordonnier 235

16 A High-Throughput Assay for DNA Topoisomerases and Other Enzymes, Based on DNA Triplex Formation Matthew R. Burrell Nicolas P. Burton Anthony Maxwell 257

17 Measurement of DNA Interstrand Crosslinking in Individual Cells Using the Single Cell Gel Electrophoresis (Comet) Assay Victoria J. Spanswick Janet M. Hartley John A. Hartley 267

18 Measurement of DNA Interstrand Crosslinking in Naked DNA Using Gel-Based Methods Konstantinos Kiakos Janet M. Hartley John A. Hartley 283

19 An Evaluation Cascade for G-Quadruplex Telomere Targeting Agents in Human Cancer Cells Mekala Gunaratnam Stephen Neidle 303

Index 315

Editorial Reviews

Reviewer: Omer Iqbal, MD, FACC, FESC (Loyola University Medical Center)
Description: This book provides authoritative and current information on the binding of new generations of DNA sequence reading compounds including triplex forming oligonucleotides and minor groove binding ligands to specific DNA sequences as anti-gene agents. This is an update of the previous edition published 12 years ago.
Purpose: This book is expected to be useful for established workers who wish to broaden their experimental repertoire, as well as for those who are new to the field and need expert advice and guidance.
Audience: The intended audience includes postgraduates, postdoctoral workers, and established scientists working in the field of drug-DNA interactions. However, even clinical investigators such as oncologists may find this book quite useful. Chapters are written by leading experts.
Features: Conveniently divided into 19 chapters, the book covers a wide range of approaches, from the cellular to the structural. The first nine chapters deal with various biophysical techniques such as thermal melting studies, capillary electrophoresis, and circular and linear dichroism of drug-DNA interactions, and other important techniques for quantifying drug-DNA interactions described in molecular and atomic detail. Other chapters cover molecular and cellular approaches of assessing the strength and mode of binding, the sequence selectivity, and their effect on biological systems. The final chapter details a series of biochemical, biophysical and cellular assays used to evaluate the activity of new compounds and to assess their suitability for examination in xenograft models of human cancer.
Assessment: This well-illustrated book of chapters written by leading experts will be extremely useful for postgraduates, post-doctoral fellows, established scientists, and some clinicians interested in the field of drug-DNA interactions. Given the significant advances in this field since the publication of the first edition in 1998, this update will be welcomed by students and justifies replacement.

Doody's Review Service

From the reviews of the second edition:

“Provides authoritative and current information on the binding of new generations of DNA sequence reading compounds … . The intended audience includes postgraduates, postdoctoral workers, and established scientists … . even clinical investigators such as oncologists may find this book quite useful. … This well-illustrated book of chapters written by leading experts will be extremely useful for postgraduates, post-doctoral fellows, established scientists, and some clinicians interested in the field of drug-DNA interactions. … this update will be welcomed by students and justifies replacement.” (Omer Iqbal, Doody’s Review Service, May, 2010)

From the Publisher

3 Stars from Doody

This book describes numerous protocols and techniques for the analysis and quantization of drug-DNA interactions. It is intended to serve as a reference for scientists interested in measuring the degree to which drugs interact with chromosomal DNA. Numerous analytical techniques are described, and the book should be of value to researchers in this field. The book has 18 chapters, compiled by 33 international experts. The techniques are current and well described. The references are up-to-date, and the illustrations are helpful and of excellent quality. To members of a rather limited audience, this book should provide a very valuable technical resource. It must be mentioned that most of the techniques deal with "weak" drug-DNA interactions such as intercalation, or ionic or hydrophobic interactions. The interaction of DNA with alkylating agents or other covalently binding compounds is treated in only one section. The editor's intent seems to be to provide an extensive treatment of methods for measuring drug-DNA intercalation, essentially omitting those methods dealing with interaction of alkylating agents. This approach does not necessarily detract from the book, rather, it sharpens its focus. However, this approach also limits the audience somewhat. The book will be very valuable to those investigating drug-DNA intercalations. It will not be valuable to those interested in covalent drug-DNA interactions.

Thomas M. Guenthner

Cookbook-style instructions describe techniques developed to explore the interaction of drugs and ligands with DNA. The methods involve sequence recognition properties, as well as the physical approaches for measuring both the strength of interaction and the mode of drug binding to DNA. Interactions are examined from a cellular perspective and for their usefulness in the design of new therapeutic agents. Annotation c. by Book News, Inc., Portland, Or.

Booknews