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Drug-DNA Interaction Protocols

  • Book
  • © 2010

Overview

Editors:
  1. Keith R. Fox

    1. School of Biological Sciences, University of Southampton, Southampton, United Kingdom

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  • Fully updated from the first edition to include up-to-date methods for studying drug-DNA interactions
  • Written by experts with hands-on experience of the techniques
  • Combines a wide range of approaches for analyzing drug-DNA interactions, from the cellular to the structural
  • Includes a collection of useful molecular techniques for exploring the interaction between ligands and DNA
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 613)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Quantitative Analysis of Small Molecule–Nucleic Acid Interactions with a Biosensor Surface and Surface Plasmon Resonance Detection

    • Yang Liu, W. David Wilson
    Pages 1-23

  3. Thermal Melting Studies of Ligand DNA Interactions

    • Aurore Guédin, Laurent Lacroix, Jean-Louis Mergny
    Pages 25-35

  4. Circular and Linear Dichroism of Drug-DNA Systems

    • Alison Rodger
    Pages 37-54

  5. Drug Binding to DNA⋅RNA Hybrid Structures

    • Richard T. Wheelhouse, Jonathan B. Chaires
    Pages 55-70

  6. Quantification of Binding Data Using Capillary Electrophoresis

    • Fitsumbirhan Araya, Graham G. Skellern, Roger D. Waigh
    Pages 71-88

  7. Determination of Equilibrium Association Constants of Ligand–DNA Complexes by Electrospray Mass Spectrometry

    • Valérie Gabelica
    Pages 89-101

  8. Detection of Adriamycin-DNA Adducts by Accelerator Mass Spectrometry

    • Kate Coldwell, Suzanne M. Cutts, Ted J. Ognibene, Paul T. Henderson, Don R. Phillips
    Pages 103-118

  9. Molecular Modelling Methods to Quantitate Drug-DNA Interactions

    • Hao Wang, Charles A. Laughton
    Pages 119-131

  10. Application of Anomalous Diffraction Methods to the Study of DNA and DNA-Complexes

    • Derrick Watkins, Tinoush Moulaei, Seiji Komeda, Loren Dean Williams
    Pages 133-152

  11. DNase I Footprinting

    • Antonia S. Cardew, Keith R. Fox
    Pages 153-172

  12. Methods to Characterize the Effect of DNA-Modifying Compounds on Nucleosomal DNA

    • Vidya Subramanian, Robert M. Williams, Dale L. Boger, Karolin Luger
    Pages 173-192

  13. REPSA: Combinatorial Approach for Identifying Preferred Drug-DNA Binding Sequences

    • Michael W. Van Dyke
    Pages 193-205

  14. In vitro Transcription Assay for Resolution of Drug-DNA Interactions at Defined DNA Sequences

    • Benny J. Evison, Don R. Phillips, Suzanne M. Cutts
    Pages 207-222

  15. In vitro Footprinting of Promoter Regions Within Supercoiled Plasmid DNA

    • Daekyu Sun
    Pages 223-233

  16. Topoisomerase I-Mediated DNA Relaxation as a Tool to Study Intercalation of Small Molecules into Supercoiled DNA

    • Paul Peixoto, Christian Bailly, Marie-Hélène David-Cordonnier
    Pages 235-256

  17. A High-Throughput Assay for DNA Topoisomerases and Other Enzymes, Based on DNA Triplex Formation

    • Matthew R. Burrell, Nicolas P. Burton, Anthony Maxwell
    Pages 257-266

  18. 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
    Pages 267-282

  19. Measurement of DNA Interstrand Crosslinking in Naked DNA Using Gel-Based Methods

    • Konstantinos Kiakos, Janet M. Hartley, John A. Hartley
    Pages 283-302

  20. An Evaluation Cascade for G-Quadruplex Telomere Targeting Agents in Human Cancer Cells

    • Mekala Gunaratnam, Stephen Neidle
    Pages 303-313
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Keywords

About this book

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.

Reviews

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)

Editors and Affiliations

  • School of Biological Sciences, University of Southampton, Southampton, United Kingdom

    Keith R. Fox

Bibliographic Information

  • Book Title: Drug-DNA Interaction Protocols

  • Editors: Keith R. Fox

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-60327-418-0

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2010

  • Hardcover ISBN: 978-1-60327-417-3Published: 17 December 2009

  • Softcover ISBN: 978-1-61779-674-6Published: 07 March 2012

  • eBook ISBN: 978-1-60327-418-0Published: 08 December 2009

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: IX, 311

  • Number of Illustrations: 102 b/w illustrations, 1 illustrations in colour

  • Additional Information: Originally published as volume 90 in the series: Methods Molecular Biology

  • Topics: Pharmacology/Toxicology, Human Genetics

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