Description
Humana Drug-Dna Interaction Protocols 2010 Edition by Keith R. Fox
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. Table of contents : Drug-DNA Interaction Protocols Second EditionEditor: Keith R. Fox PhDContentsPrefaceContributors1. Quantitative Analysis of Small Molecule- Nucleic Acid Interactions with a Biosensor Surface and Surface Plasmon Resonance DetectionYang Liu and W. David Wilson 2. Thermal Melting Studies of Ligand DNA InteractionsAurore Guedin Laurent Lacroix and Jean-Louis Mergny3. Circular and Linear Dichroism of Drug-DNA SystemsAlison Rodger4. Drug Binding to DNA*RNA Hybrid StructuresRichard T. Wheelhouse and Jonathan B. Chaires5. Quantification of Binding Data Using Capillary ElectrophoresisFitsumbirhan Araya Graham G. Skellern and Roger D. Waigh6. Determination of Equilibrium Association Constants of Ligand-DNA Complexes by Electrospray Mass SpectrometryValerie Gabelica7. Detection of Adriamycin-DNA Adducts by Accelerator Mass Spectrometry Kate Coldwell Suzanne M. Cutts Ted J. Ognibene Paul T. Henderson and Don R. Phillips8. Molecular Modelling Methods to Quantitate Drug-DNA InteractionsHao Wang and Charles A. Laughton9. Application of Anomalous Diffraction Methods to the Study of DNA and DNA-ComplexesDerrick Watkins Tinoush Moulaei Seiji Komeda and Loren Dean Williams10. DNase I Footprinting.Antonia S. Cardew and Keith R. Fox11. Methods to Characterize the Effect of DNA-Modifying Compounds on Nucleosomal DNAVidya Subramanian Robert M. Williams Dale L. Boger and Karolin Luger12. REPSA: Combinatorial Approach for Identifying Preferred Drug-DNA Binding SequencesMichael W. Van Dyke13. In Vitro Transcription Assay for Resolution of Drug-DNA Interactions at Defined DNA SequencesBenny J. Evison Don R. Phillips and Suzanne M.Cutts14. In Vitro Footprinting of Promoter Regions within Supercoiled Plasmid DNADaekyu Sun15. Topoisomerase I-Mediated DNA Relaxation as a Tool to Study Intercalation of Small Molecules into Supercoiled DNAPaul Peixoto Christian Bailly and Marie-Helene David-Cordonnier16. A High-Throughput Assay for DNA Topoisomerases and Other Enzymes Based on DNA Triplex Formation.Matthew R. Burrell Nicolas P. Burton and Anthony Maxwell17. Measurement of DNA Interstrand Crosslinking in Individual Cells Using the Single Cell Gel Electrophoresis (Comet) AssayVictoria J. Spanswick Janet M. Hartley and John A. Hartley18. Measurement of DNA Interstrand Crosslinking in Naked DNA Using Gel-Based MethodsKonstantinos Kiakos Janet M. Hartley and John A. Hartley19. An Evaluation Cascade for G-Quadruplex Telomere Targeting Agents in Human Cancer CellsMekala Gunaratnam and Stephen Neidle