Main description:

This volume covers the structures, properties, and functions of G-quadruplexes in a wide range of biological disciplines, including therapeutic intervention and biomaterial application. The chapters in this book explore a wide range of vital and new experimental techniques used in the study of G-quadruplexes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Practical and cutting-edge, G-Quadruplex DNA: Methods and Protocols is a valuable resource for both novice and experienced researchers who work in biophysics, structural biology, computational biology, biochemistry, and molecular and cell biology, and who want to learn more about the potential roles and effects of G-quadruplex in these fields.

Contents:

Preface...Table of Contents...Contributing Authors...
1. G-Quadruplex DNA and RNADanzhou Yang
2. CD Study of the G-Quadruplex ConformationIva Kejnovska, Daniel Renciuk, Jan Palacky, and Michaela Vorlickova
3. Revealing the Energetics of Ligand-Quadruplex Interactions using Isothermal Titration CalorimetryAndrea Funke and Klaus Weisz
4. Biosensor-Surface Plasmon Resonance: Label Free Method for Investigation of Small Molecule-Quadruplex Nucleic Acid InteractionsAnanya Paul, Caterina Musetti, Rupesh Nanjunda, and W. David Wilson
5. Putting a New Spin of G-Quadruplex Structure and Binding by Analytical UltracentrifugationWilliam L. Dean, Robert D. Gray, Lynn DeLeeuw, Robert C. Monsen, and Jonathan B. Chaires
6. Mass Spectroscopic Study of G-QuadruplexHuihui Li
7. G-Quadruplex Stability from DSC MeasurementsSan Hadzi, Matjaz Boncina, and Jurij Lah
8. X-Ray Crystallographic Studies of G-Quadruplex StructuresGary N. Parkinson and Gavin W. Collie
9. NMR Studies of G-Quadruplex Structures and G-Quadruplex-Interactive CompoundsClement Lin, Jonathan Dickerhoff, and Danzhou Yang
10. Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex LigandsNanjie Deng
11. Electrophoretic Mobility Shift Assay and Dimethyl Sulfate Footprinting for Characterization of G-Quadruplexes and G-Quadruplex-Protein ComplexesBuket Onel, Guanhui Wu, Daekyu Sun, Clement Lin, and Danzhou Yang
12. A DNA Polymerase Stop Assay for Characterization of G-Quadruplex Formation and Identification of G-Quadruplex-Interactive Compounds Guanhui Wu and Haiyong Han
13. Chromatin Immunoprecipitation Assay to Analyze the Effect of G-Quadruplex Interactive Agents on the Binding of RNA Polymerase II and Transcription Factors to a Target Promoter Region Daekyu Sun
14. Characterization of Co-Transcriptional Formation of G-Quadruplexes in Double-Stranded DNA Ke-wei Zheng, Jia-yu Zhang, and Zheng Tan
15. Quantitative Analysis of Stall of Replicating DNA Polymerase by G-Quadruplex Formation Shuntaro Takahashi and Naoki Sugimoto
16. Single-Molecule Investigations of G-QuadruplexShankar Mandal, Mohammed Enamul Hoque, and Hanbin Mao
17. Direct Observation of the Formation and Dissociation of Double-Stranded DNA Containing G-Quadruplex/i-motif Sequences in the DNA Origami Frame using High-Speed AFMMasayuki Endo, Xiwen Xing, and Hiroshi Sugiyama
18. G-Quadruplex and Protein Binding by Single-Molecule FRET Microscopy Chun-Ying Lee, Christina McNerney, and Sua Myong
19. High-Throughput Screening of G-Quadruplex Ligands by FRET AssayKaibo Wang, Daniel P. Flaherty, Lan Chen, and Danzhou Yang
20. Targeting G-Quadruplexes with PNA OligomersBruce A. Armitage
21. Primer-Modified G-Quadruplex-Au Nanoparticles for Colorimetric Assay of Human Telomerase Activity and Initial Screening of Telomerase InhibitorsFang Pu, Jinsong Ren, and Xiaogang Qu
22. Heme*G-Quadruplex DNAzymes: Conditions for Maximizing their Peroxidase ActivityNisreen Shumayrikh and Dipankar Sen
23. In Vivo Chemical Probing for G-Quadruplex FormationFedor Kouzine, Damian Wojtowicz, Arito Yamane, Rafael Casellas, Teresa M. Przytycka, and David L. Levens
24. G-Quadruplex Visualization In Cells via Antibody and Fluorescence ProbeMatteo Nadai and Sara N. Richter
25. In Cell NMR Spectroscopy: Investigation of G-Quadruplex Structures inside Living Xenopus laevis OocytesMichaela Krafcikova, Robert Hansel-Hertsch, Lukas Trantirek, and Silvie Foldynova-Trantirkova
26. 19F NMR Spectroscopy for the Analysis of DNA G-Quadruplex Structures using 19F-labeled NucleobaseTakumi Ishizuka, Hong-Liang Bao, and Yan Xu