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G-Quadruplex Nucleic Acids

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Danzhou Yang

    1. Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Clement Lin

    1. Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2035)

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. G-Quadruplex DNA and RNA

    • Danzhou Yang
    Pages 1-24

  3. CD Study of the G-Quadruplex Conformation

    • Iva Kejnovská, Daniel Renčiuk, Jan Palacký, Michaela Vorlíčková
    Pages 25-44

  4. Revealing the Energetics of Ligand-Quadruplex Interactions Using Isothermal Titration Calorimetry

    • Andrea Funke, Klaus Weisz
    Pages 45-61

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

    • Ananya Paul, Caterina Musetti, Rupesh Nanjunda, W. David Wilson
    Pages 63-85

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

    • William L. Dean, Robert D. Gray, Lynn DeLeeuw, Robert C. Monsen, Jonathan B. Chaires
    Pages 87-103

  7. Mass Spectroscopic Study of G-Quadruplex

    • Huihui Li
    Pages 105-116

  8. G-Quadruplex Stability from DSC Measurements

    • San Hadži, Matjaž Bončina, Jurij Lah
    Pages 117-130

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

    • Gary N. Parkinson, Gavin W. Collie
    Pages 131-155

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

    • Clement Lin, Jonathan Dickerhoff, Danzhou Yang
    Pages 157-176

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

    • Nanjie Deng
    Pages 177-199

  12. 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, Danzhou Yang
    Pages 201-222

  13. A DNA Polymerase Stop Assay for Characterization of G-Quadruplex Formation and Identification of G-Quadruplex-Interactive Compounds

    • Guanhui Wu, Haiyong Han
    Pages 223-231

  14. 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
    Pages 233-242

  15. Characterization of Co-transcriptional Formation of G-Quadruplexes in Double-Stranded DNA

    • Ke-wei Zheng, Jia-yu Zhang, Zheng Tan
    Pages 243-255

  16. Quantitative Analysis of Stall of Replicating DNA Polymerase by G-Quadruplex Formation

    • Shuntaro Takahashi, Naoki Sugimoto
    Pages 257-274

  17. Single-Molecule Investigations of G-Quadruplex

    • Shankar Mandal, Mohammed Enamul Hoque, Hanbin Mao
    Pages 275-298

  18. 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, Hiroshi Sugiyama
    Pages 299-308

  19. G-Quadruplex and Protein Binding by Single-Molecule FRET Microscopy

    • Chun-Ying Lee, Christina McNerney, Sua Myong
    Pages 309-322

  20. High-Throughput Screening of G-Quadruplex Ligands by FRET Assay

    • Kaibo Wang, Daniel P. Flaherty, Lan Chen, Danzhou Yang
    Pages 323-331
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Keywords

About this book

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. 



Editors and Affiliations

  • Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, USA

    Danzhou Yang

  • Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, USA

    Clement Lin

Bibliographic Information

  • Book Title: G-Quadruplex Nucleic Acids

  • Book Subtitle: Methods and Protocols

  • Editors: Danzhou Yang, Clement Lin

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9666-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9665-0Published: 24 August 2019

  • Softcover ISBN: 978-1-4939-9668-1Published: 25 August 2020

  • eBook ISBN: 978-1-4939-9666-7Published: 23 August 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 437

  • Number of Illustrations: 26 b/w illustrations, 95 illustrations in colour

  • Topics: Human Genetics, Mass Spectrometry

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