A collection of useful molecular techniques to illuminate and explore the interaction of drugs and ligands with DNA. These easily reproducible 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. The interactions are also examined from a cellular perspective and for their usefulness in the design of new therapeutic agents. The powerful techniques detailed here will be particularly useful in elucidating the action of existing therapeutic agents, as well as in the design of new anti-cancer drugs with improved action and reduced toxicity.

Table of Contents:
DNase I FootprintingKeith R. FoxQuantitative DNA FootprintingJames C. Dabrowiak, Jerry Goodisman, and Brian WardUranyl Photoprobing of DNA Structures and Drug-DNA ComplexesNiels Erik Mollegard and Peter E. NielsenDiethylpyrocarbonate and Osmium Tetroxide as Probes for Drug-Induced Changes in DNA Conformation In VitroChristian Bailly and Michael J. WaringFootprinting Studies with Nucleosome-Bound DNAPhilip M. Brown and Keith R. FoxA Gel Mobility Shift Assay for Probing the Effect of Drug-DNA Adducts on DNA-Binding ProteinsSuzanne M. Cutts, Andrew Masta, Con Panousis, Peter G. Parsons, Richard A. Sturm, and Don R. PhillipsAn Oligonucleotide Crosslinking Assay for the Analysis of Individual Drug-Binding SitesSuzanne M. Cutts, Con Panousis, Andrew Masta, and Don R. PhillipsDNA Polymerase Inhibition Assay (PIA) for the Detection of Drug-DNA InteractionsThomas P. Dooley and Katherine L. WeilandTranscriptional Footprinting of Drug-DNA InteractionsDon R. Phillips and Carleen CullinaneDetermination of the DNA Sequence Specificity of Alkylation Damage Using Cleavage-Based AssaysJohn A. Hartley and Michael D. WyattPCR-Based Methods for Detecting DNA Damage and Its Repair at the Subgene and Single Nucleotide Levels in CellsKeith A. Grimaldi and John A. HartleyAnalysis of DNA-Binding AntibodiesJeremy S. Lee, Laura J. P. Latimer, and Jamshid TanhaImmunofluorescent Staining of Chromosomes with DNA-Binding AntibodiesJeremy S. Lee, Laura J. P. Latimer, and Gary D. BurkholderOptical Absorbance and Fluorescence Techniques for Measuring DNA-Drug InteractionsTerence C. JenkinsEvaluation of Drug-Nucleic Acid Interactions by Thermal Melting CurvesW. David Wilson, Farial A. Tanious, Maria Fernandez-Saiz, and C. Ted RiglElectric DichroismDietmar PorschkeCalorimetric Techniques for Studying Drug-DNA InteractionsHarry P. Hopkins, JrMethods for the Studies of Drug Dissociation from DNAFu-Ming ChenIndex