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G4 biology
- 1st Edition, Volume 695 - March 21, 2024
- Editors: Kevin D Raney, Robert Eoff, Alicia Byrd, Samantha Kendrick
- Language: English
- Hardback ISBN:9 7 8 - 0 - 4 4 3 - 2 1 7 7 4 - 6
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 2 1 7 7 5 - 3
G4 Biology, Volume 695 in the Methods in Enzymology series, highlights high value topics such as Assays to measure G4 resolution by DNA helicases, In gel staining methods of G4 DN… Read more
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Request a sales quoteG4 Biology, Volume 695 in the Methods in Enzymology series, highlights high value topics such as Assays to measure G4 resolution by DNA helicases, In gel staining methods of G4 DNA and RNA structures, Methods to probe the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution, Analyzing the effect of transcription coupled R-loop formation on G4 formation, Integrated Structural Biology for the study of higher-order G4 structures, Advancing the Study of Protein-G4 Interactions in DNA Repair: Insights from Biolayer Interferometry and Circular Dichroism Spectroscopy, Immunofluorescence microscopy (IF) of G-quadruplex and R-loops, and more.
Additional chapters delve into Production of the anti-G-quadruplex antibody BG4 for efficient ChIP-seq and CUT&Tag analysis: from plasmid quality control to validation, Utility of intercalator displacement assays for screening of ligands for i-motif DNA structures, Potentiometric titrations to study ligand interactions with DNA i-motifs, Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy, and Identification of bona fide G4-binding proteins, Observing Pif1 opening dsDNA and G4 in real time by manipulation under magnetic tweezers, and in vivo detection of DNA secondary structures using Permanganate/S1 Footprinting with direct adapter ligation and sequencing (PDAL-Seq).
- Provides the authority and expertise of leading contributors from an international board of authors
- Presents the latest release in Methods in Enzymology series
- Updated release includes the latest information on G4 biology
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists
- Cover image
- Title page
- Table of Contents
- Series Page
- Copyright
- Contributors
- G4 and i-motif Biology
- Chapter One: Purification and biochemical characterization of the G4 resolvase and DNA helicase FANCJ
- Abstract
- 1 Introduction
- 2 Before you begin
- 3 Key resources table
- 4 Materials and equipment
- 5 Reagents
- 6 Step-by-step method details
- 7 Preparation of radiolabeled forked duplex DNA substrate
- 8 Preparation of G-quadruplex DNA substrates
- 9 Radiometric helicase assay
- 10 Image acquisition and analysis
- 11 Expected outcomes
- 12 Quantification and statistical analysis
- 13 Advantages
- 14 Limitations
- 15 Optimization and troubleshooting
- 16 Safety considerations and standards
- 17 Concluding remarks
- Acknowledgments
- References
- Chapter Two: In-gel staining methods of G4 DNA and RNA structures
- Abstract
- 1 Introduction
- 2 Before you begin
- 3 Key resources table
- 4 Materials and equipment
- 5 Step-by-step method details
- 6 Expected outcomes
- 7 Quantification and statistical analysis
- 8 Advantages
- 9 Limitations
- 10 Optimization and troubleshooting
- 11 Safety considerations and standards
- Acknowledgment
- References
- Chapter Three: A beginner’s handbook to identify and characterize i-motif DNA
- Abstract
- 1 Introduction
- 2 General methods and analyses
- 3 Preparation of oligonucleotides
- 4 Circular dichroism (CD) spectroscopy
- 5 1D 1H nuclear magnetic resonance (NMR) spectroscopy
- 6 High resolution primer extension assay
- 7 Summary and conclusions
- Acknowledgment
- References
- Chapter Four: Single-molecule observation of G-quadruplex and R-loop formation induced by transcription
- Abstract
- 1 Introduction
- 2 Equipment
- 3 Reagents
- 4 Experimental preparation for real-time observation of cotranscriptional G4 and R-loop formation
- 5 Experimental preparation to investigate the mechanism of transcription regulation by G4/R-loop formation
- 6 Conclusion
- Acknowledgment
- References
- Chapter Five: Advancing the study of protein-G4 interactions in DNA repair: Insights from biolayer interferometry
- Abstract
- 1 Introduction
- 2 Major considerations
- 3 Material and equipment
- 4 BLI binding assay
- 5 Conclusions
- Acknowledgments
- References
- Chapter Six: Immunofluorescence microscopy of G-quadruplexes and R-loops
- Abstract
- 1 Introduction
- 2 Materials and equipment
- 3 Procedures
- 4 Summary and conclusions
- Acknowledgments
- References
- Chapter Seven: Observing G4 formation and its resolution by Pif1 in real time by manipulation under magnetic tweezers
- Abstract
- 1 Introduction
- 2 Formation and observation of G4 structure in a double-stranded context
- 3 Observation of helicase activity in a DNA hairpin
- 4 Discussion
- Funding
- References
- Chapter Eight: In vivo detection of DNA secondary structures using permanganate/S1 footprinting with direct adapter ligation and sequencing (PDAL-Seq)
- Abstract
- 1 Introduction
- 2 Technical details: choosing the appropriate potassium permanganate and S1 concentrations
- 3 Method description
- Acknowledgments
- References
- Chapter Nine: Production of the anti-G-quadruplex antibody BG4 for efficient genome-wide analyses: From plasmid quality control to antibody validation
- Abstract
- 1 Introduction
- 2 Before you begin timing: 5–7 days
- 3 pSANG10-3F-BG4 plasmid quality control
- 4 pSANG10-3F-BG4 plasmid transformation and antibody expression induction
- 5 Bacterial cells lysis and antibody purification
- 6 Assessment of BG4 in the eluted fractions VIA coomassie staining
- 7 BG4 dialysis and antibody concentration
- 8 Validation of BG4 activity
- 9 Applications of BG4 for genome-wide identification of G4 structures
- References
- Chapter Ten: Utility of intercalator displacement assays for screening of ligands for i-motif DNA structures
- Abstract
- 1 Introduction
- 2 Reagents, materials, and equipment
- 3 Buffer and sample preparations
- 4 Experimental protocol
- 5 Troubleshooting
- 6 Summary
- References
- Chapter Eleven: Potentiometric titrations to study ligand interactions with DNA i-motifs
- Abstract
- 1 Introduction
- 2 Experimental setup for potentiometric CD titrations
- 3 Experimental protocol
- 4 Data analysis
- 5 Examples
- 6 Conclusions
- Acknowledgments
- References
- Chapter Twelve: Identification of bona fide RNA G-quadruplex binding proteins
- Abstract
- 1 Introduction
- 2 General methods
- 3 Summary and conclusion
- Acknowledgment
- References
- No. of pages: 412
- Language: English
- Edition: 1
- Volume: 695
- Published: March 21, 2024
- Imprint: Academic Press
- Hardback ISBN: 9780443217746
- eBook ISBN: 9780443217753
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