Preface ......................................................... v
Contributors ................................................... ix
1 Quantitative Analysis of Small Molecule-Nucleic Acid
Interactions with a Biosensor Surface and Surface Plasmon
Resonance Detection .......................................... 1
Yang Liu and W. David Wilson
2 Thermal Melting Studies of Ligand DNA Interactions .......... 25
Aurore Guédin, Laurent Lacroix, and Jean-Louis Mergny
3 Circular and Linear Dichroism of Drug-DNA Systems ........... 37
Alison Rodger
4 Drug Binding to DNA-RNA Hybrid Structures ................... 55
Richard T. Wheelhouse and Jonathan B. Chaires
5 Quantification of Binding Data Using Capillary
Electrophoresis ............................................. 71
Pitsumbirhan Araya, Graham G. Skellern, and Roger D. Waigh
6 Determination of Equilibrium Association Constants of
Ligand-DNA Complexes by Electrospray Mass Spectrometry ...... 89
Valérie Gabelica
7 Detection of Adriamycin-DNA Adducts by Accelerator Mass
Spectrometry ............................................... 103
Kate Coldwell, Suzanne M. Cutts, Ted J. Ognibene, Paul
T. Henderson, and Don R. Phillips
8 Molecular Modelling Methods to Quantitate Drug-DNA
Interactions ............................................... 119
Hao Wang and Charles A. Laughton
9 Application of Anomalous Diffraction Methods to the Study
of DNA and DNA-Complexes ................................... 133
Derrick Watkins, Tinoush Moulaei, Seiji Komeda, and
Loren Dean Williams
10 DNase I Footprinting ...................................... 153
Antonia S. Cardew and Keith R. Fox
11 Methods to Characterize the Effect of DNA-Modifying
Compounds on Nucleosomal DNA ............................... 173
Vidya Subramanian, Robert M. Williams, Dale L. Boger,
and Karolin Luger
12 REPSA: Combinatorial Approach for Identifying Preferred
Drug-DNA Binding Sequences ................................ 193
Michael W. Van Dyke
13 In vitro Transcription Assay for Resolution of Drug-DNA
Interactions at Defined DNA Sequences ...................... 207
Benny J. Evison, Don R. Phillips, and Suzanne M. Cutts
14 In vitro Footprinting of Promoter Regions Within
Supercoiled Plasmid DNA .................................... 223
Daekyu Sun
15 Topoisomerase I-Mediated DNA Relaxation as a Tool to
Study Intercalation of Small Molecules into Supercoiled
DNA ........................................................ 235
Paul Peixoto, Christian Bailly, and Marie-Hélène David-
Cordonnier
16 A High-Throughput Assay for DNA Topoisomerases and Other
Enzymes, Based on DNA Triplex Formation .................... 257
Matthew R. Burrell, Nicolas P. Burton, and Anthony
Maxwell
17 Measurement of DNA Interstrand Crosslinking in Individual
Cells Using the Single Cell Gel Electrophoresis (Comet)
Assay ...................................................... 267
Victoria J. Spanswick, Janet M. Hartley, and John
A. Hartley
18 Measurement of DNA Interstrand Crosslinking in Naked DNA
Using Gel-Based Methods ................................... 283
Konstantinos Kiakos, Janet M. Hartley, and John
A. Hartley
19 An Evaluation Cascade for G-Quadruplex Telomere Targeting
Agents in Human Cancer Cells ............................... 303
Mekala Gunaratnam and Stephen Neidle
Index ........................................................ 315
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