Quantitative Analysis of Small Molecule-Nucleic Acid Interactions with a Biosensor Surface and Surface Plasmon Resonance Detection -- Thermal Melting Studies of Ligand DNA Interactions -- Circular and Linear Dichroism of Drug-DNA Systems -- Drug Binding to DNA?RNA Hybrid Structures -- Quantification of Binding Data Using Capillary Electrophoresis -- Determination of Equilibrium Association Constants of Ligand-DNA Complexes by Electrospray Mass Spectrometry -- Detection of Adriamycin-DNA Adducts by Accelerator Mass Spectrometry -- Molecular Modelling Methods to Quantitate Drug-DNA Interactions -- Application of Anomalous Diffraction Methods to the Study of DNA and DNA-Complexes -- DNase I Footprinting -- Methods to Characterize the Effect of DNA-Modifying Compounds on Nucleosomal DNA -- REPSA: Combinatorial Approach for Identifying Preferred Drug-DNA Binding Sequences -- In vitro Transcription Assay for Resolution of Drug-DNA Interactions at Defined DNA Sequences -- In vitro Footprinting of Promoter Regions Within Supercoiled Plasmid DNA -- Topoisomerase I-Mediated DNA Relaxation as a Tool to Study Intercalation of Small Molecules into Supercoiled DNA -- A High-Throughput Assay for DNA Topoisomerases and Other Enzymes, Based on DNA Triplex Formation -- Measurement of DNA Interstrand Crosslinking in Individual Cells Using the Single Cell Gel Electrophoresis (Comet) Assay -- Measurement of DNA Interstrand Crosslinking in Naked DNA Using Gel-Based Methods -- An Evaluation Cascade for G-Quadruplex Telomere Targeting Agents in Human Cancer Cells.

The last few years have witnessed the creation of new generations of sequence reading compounds, which have incredible potential for targeting specific DNA sequences. In Drug-DNA Interaction Protocols, Second Edition, expert researchers explore these compounds, revealing how a deeper understanding of the structure of DNA, along with an improved ability to manipulate it, has led to much progress in recent years. Chapters describe a new arsenal of techniques for probing the interactions between drugs and DNA, including various biophysical techniques for quantifying these interactions and for describing them in molecular and atomic detail, and they comprehensively consider both molecular and cellular approaches. Composed in the highly successful Methods in Molecular Biology™ series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Authoritative and current, Drug-DNA Interaction Protocols, Second Edition, is a critical volume that includes a wide range of chapters, which together provide methods for assessing the strength and mode of binding, the sequence selectivity, and the effect on biological systems.