Drug-DNA Interaction Protocols

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 this authoritative and current book, expert researchers explore these compounds.

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.

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

Inhalt
Quantitative Analysis of Small MoleculeNucleic 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 LigandDNA 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.