G-Quadruplex Nucleic Acids: Methods and Protocols

ISBN-13: 9781493996681 / Angielski / Miękka / 2020 / 437 str.

Danzhou Yang; Clement Lin

Spis treści

Preface…

Table of Contents…

Contributing Authors…

1. G-Quadruplex DNA and RNA

Danzhou Yang

2. CD Study of the G-Quadruplex Conformation

Iva Kejnovská, Daniel Renčiuk, Jan Palacký, and Michaela Vorlíčková

3. Revealing the Energetics of Ligand-Quadruplex Interactions using Isothermal Titration Calorimetry

Andrea Funke and Klaus Weisz 

4. Biosensor-Surface Plasmon Resonance: Label Free Method for Investigation of Small Molecule-Quadruplex Nucleic Acid Interactions

Ananya Paul, Caterina Musetti, Rupesh Nanjunda, and W. David Wilson

5. Putting a New Spin of G-Quadruplex Structure and Binding by Analytical Ultracentrifugation

William L. Dean, Robert D. Gray, Lynn DeLeeuw, Robert C. Monsen, and Jonathan B. Chaires

6. Mass Spectroscopic Study of G-Quadruplex

Huihui Li

7. G-Quadruplex Stability from DSC Measurements

San Hadži, Matjaž Bončina, and Jurij Lah

8. X-Ray Crystallographic Studies of G-Quadruplex Structures

Gary N. Parkinson and Gavin W. Collie

9. NMR Studies of G-Quadruplex Structures and G-Quadruplex-Interactive Compounds

Clement Lin, Jonathan Dickerhoff, and Danzhou Yang

10. Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex Ligands

Nanjie Deng

11. Electrophoretic Mobility Shift Assay and Dimethyl Sulfate Footprinting for Characterization of G-Quadruplexes and G-Quadruplex-Protein Complexes

Buket 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-Quadruplex

Shankar 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 AFM

Masayuki 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 Assay

Kaibo Wang, Daniel P. Flaherty, Lan Chen, and Danzhou Yang

20. Targeting G-Quadruplexes with PNA Oligomers

Bruce A. Armitage

21. Primer-Modified G-Quadruplex-Au Nanoparticles for Colorimetric Assay of Human Telomerase Activity and Initial Screening of Telomerase Inhibitors

Fang Pu, Jinsong Ren, and Xiaogang Qu

22. Heme•G-Quadruplex DNAzymes: Conditions for Maximizing their Peroxidase Activity

Nisreen Shumayrikh and Dipankar Sen

23. In Vivo Chemical Probing for G-Quadruplex Formation

Fedor Kouzine, Damian Wojtowicz, Arito Yamane, Rafael Casellas, Teresa M. Przytycka, and David L. Levens 

24. G-Quadruplex Visualization In Cells via Antibody and Fluorescence Probe

Matteo Nadai and Sara N. Richter

25. In Cell NMR Spectroscopy: Investigation of G-Quadruplex Structures inside Living Xenopus laevis Oocytes

Michaela Krafcikova, Robert Hänsel-Hertsch, Lukas Trantirek, and Silvie Foldynova-Trantirkova

26. 19F NMR Spectroscopy for the Analysis of DNA G-Quadruplex Structures using 19F-labeled Nucleobase

Takumi Ishizuka, Hong-Liang Bao, and Yan Xu

Blurb

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.