G-Quadruplex DNA Methods and Protocols

Recent work has revealed that stabilizing G-quadruplexes in telomeric DNA inhibits telomerase activity, providing impetus for the development of G-quartet-interacting drugs, while G-quartet-containing oligonucleotides have been recognized as a potent class of aptamers effective against STAT3 and other transcription factors implicated in oncogenesis, proving these guanine-quartets to be a vital and rich area for future study. In "G-Quadruplex DNA: Methods and Protocols", experts in the field present a collection of detailed techniques for studying G-quartet formation, dynamics, and molecular recognition. Written in the highly successful Methods in Molecular Biology™ series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, "G-Quadruplex DNA: Methods and Protocols "promises to be a useful resource for those familiar with G-quartets as well as an easy entry point for those researchers from diverse fields who are just developing an interest in the exciting implications of G-quadruplex DNA.

1. G-Quadruplexes: From Guanine Gels to Chemotherapeutics Tracy M. Bryan and Peter Baumann 2. Molecular Modeling and Simulation of G-Quadruplexes and Quadruplex-Ligand Complexes Shozeb Haider and Stephen Neidle 3. Computational Approaches to the Detection and Analysis of Sequences with Intramolecular G-Quadruplex Forming Potential Paul Ryvkin, Steve G. Hershman, Li-San Wang, and F. Brad Johnson 4. Preparation of G-Quartet Structures and Detection by Native Gel Electrophoresis Ian K. Moon and Michael B. Jarstfer 5. Biochemical Techniques for the Characterization of G-Quadruplex Structures: EMSA, DMS Footprinting, and DNA Polymerase Stop Assay Daekyu Sun and Laurence H. Hurley 6. Real-time Observation of G-Quadruplex Dynamics Using Single Molecule FRET Microscopy Burak Okumus and Taekjip Ha 7. Sedimentation Velocity Ultracentrifugation Analysis for Hydrodynamic Characterization of G-Quadruplex Structures Nichola C. Garbett, Chongkham S. Mekmaysy, and Jonathan B. Chaires 8. 2-Aminopurine as a Probe for Quadruplex Loop Structures Robert D. Gray, Luigi Pettracone, Robert Buscaglia, and Jonathan B. Chaires 9. Assessing DNA Structures with 125I Radioprobing Timur I. Gaynutdinov, Ronald D. Neumann, and Igor G. Panyutin 10. Monitoring the Temperature Unfolding of G-Quadruplexes by UV and Circular Dichroism Spectroscopies and Calorimetry Techniques Chris M. Olsen and Luis A. Marky 11. Probing Telomeric G-Quadruplex DNA Structures in Cells with in vitro Generated Single-Chain Antibody Fragments Christiane Schaffitzel, Jan Postberg, Katrin Paeschke, and Hans J. Lipps 12. Detection of G-Quadruplexes in Cells and Investigation of G-Quadruplex Structure of d(T2AG3)4 in K+ Solution by a Carbazole Derivative: BMVC Ta-Chau Chang and Cheng-Chung Chang 13. Isolation of G-Quadruplex DNA Using NMM-Sepharose Affinity Chromatography Jasmine S. Smith and F. Brad Johnson 14. Quantifying Interactions between G-Quadruplex DNA and Transition Metal Complexes Roxanne Kieltyka, Pablo Englebienne, Nicolas Moitessier, and Hanadi Sleiman 15. G4-FID: A Fluorescent DNA Probe Displacement Assay for Rapid Evaluation of Quadruplex Ligands David Monchaud and Marie-Paule Teulade-Fichou