Helicase Enzymes Part B
- 1st Edition - August 12, 2022
- Imprint: Academic Press
- Editor: Michael Trakselis
- Language: English
- Hardback ISBN:9 7 8 - 0 - 3 2 3 - 9 9 7 7 3 - 7
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 9 7 7 4 - 4
Methods in Enzymology serial highlights new advances in the field with this new volume presenting interesting chapters. Each chapter is written by an international board of author… Read more
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Request a sales quoteMethods in Enzymology serial highlights new advances in the field with this new volume presenting interesting chapters. Each chapter is written by an international board of authors.
- Provides the authority and expertise of leading contributors from an international board of authors
- Presents the latest release in Methods in Enzymology serials
- Updated release includes the latest information on Helicase Enzymes
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists
- Cover
- Title page
- Table of Contents
- Copyright
- Contributors
- Preface
- Chapter One: Fluorescence approaches for biochemical analysis of ATP-dependent chromatin remodeling enzymes
- Abstract
- 1: Introduction
- 2: Determining substrate affinity utilizing fluorescence polarization
- 3: Determining remodeling rates using Förster resonance energy transfer (FRET)
- 4: Summary and conclusions
- Acknowledgments
- References
- Chapter Two: Attacking a DEAD problem: The role of DEAD-box ATPases in ribosome assembly and beyond
- Abstract
- 1: Introduction
- 2: DEAD-box proteins tend to remodel RNA-protein interactions in vivo
- 3: A roadmap for the discovery of biological roles for DEAD-box proteins
- 4: Summary and outlook
- Acknowledgments
- References
- Chapter Three: Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study
- Abstract
- 1: Introduction
- 2: NADH-coupled ATPase assay to measure RNA binding affinity
- 3: Summary
- Acknowledgments
- References
- Chapter Four: Measurement of ATP utilization in RNA unwinding and RNA chaperone activities by DEAD-box helicase proteins
- Abstract
- 1: Introduction
- 2: ATP utilization in RNA unwinding reactions
- 3: ATP utilization in RNA chaperone/refolding reactions
- 4: Conclusion
- Acknowledgments
- References
- Chapter Five: In vitro characterization of Dhr1 from Saccharomyces cerevisiae
- Abstract
- 1: Introduction
- 2: Biochemical characterization of Dhr1
- 3: Expression and purification of full-length Dhr1 from yeast
- 4: Expression and purification of N-terminally truncated Dhr1
- 5: Microtiter plate assay for RNA-dependent ATPase activity
- 6: U3-ETS2 duplex unwinding assays under pre-steady state conditions
- 7: Summary and conclusions
- References
- Chapter Six: Translational control by helicases during cellular stress
- Abstract
- 1: Introduction
- 2: General reagents and conditions
- 3: Growth assays to assess stress phenotypes
- 4: Translation assays to assess stress phenotypes
- 5: Other general protocols
- 6: Summary and conclusion
- Acknowledgments
- References
- Chapter Seven: Lysate and cell-based assays to probe the translational role of RNA helicases
- Abstract
- 1: Introduction
- 2: Before you begin
- 3: Step-by-step method details
- 4: Quantification and statistical analysis
- 5: Expected outcomes
- 6: Advantages and limitations
- 7: Optimization and troubleshooting
- 8: Alternative methods/procedures
- 9: Summary and conclusion
- Acknowledgments
- References
- Chapter Eight: Bulk phase biochemistry of PIF1 and RecQ4 family helicases
- Abstract
- 1: Introduction
- 2: Before you begin
- 3: Materials and equipment
- 4: Step-by-step method details
- References
- Chapter Nine: Biochemical and single-molecule techniques to study accessory helicase resolution of R-loop proteins at stalled replication forks
- Abstract
- 1: Introduction
- 2: Using dCas9 as a model R-loop protein block to replication
- 3: Purification of Pif1 helicase
- 4: Biochemical reconstitution of Pif1 clearance of R-loop stalled replication forks
- 5: Single-molecule observation of Pif1 clearance of R-loop stalled replication forks
- 6: Overview and conclusion
- Acknowledgments
- References
- Chapter Ten: Transcriptional regulation by a RecQ helicase
- Abstract
- 1: Introduction
- 2: Experimental approach and applications
- 3: Material and equipment
- 4: Methods
- 5: Notes
- Acknowledgments
- References
- Chapter Eleven: Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on surfaces
- Abstract
- 1: Introduction
- 2: Förster resonance energy transfer (FRET) as a molecular ruler
- 3: Strategies in the experimental design of single-molecule FRET studies
- 4: Confocal microscopy on helicases in solution: Equilibrium distributions of conformers
- 5: Total internal reflection microscopy: Kinetics of conformational changes
- 6: Conclusions
- References
- Chapter Twelve: Long DNA constructs to study helicases and nucleic acid translocases using optical tweezers
- Abstract
- 1: Introduction
- 2: Molecular design of large DNA plasmids
- 3: Fabrication of long double-stranded DNA constructs from large plasmids
- 4: Case 1: A hybrid ssDNA-dsDNA construct for single-molecule experiments
- 5: Case 2: A pure single-stranded DNA construct for single molecule experiments
- 6: Case 3: A flap dsDNA construct for single molecule experiments
- 7: Long DNA constructs for the study of human HELB in C-trap experiments
- 8: Summary and conclusions
- Acknowledgments
- References
- Chapter Thirteen: Novel approaches to study helicases using magnetic tweezers
- Abstract
- 1: Introduction
- 2: Advances in synthesis, attachment and calibration of nucleic acid hairpins for magnetic tweezer experiments
- 3: Advanced protocols for helicase characterization using magnetic tweezers
- 4: Discussion
- References
- Chapter Fourteen: Reconstitution and biochemical characterization of the RNA-guided helicase-nuclease protein Cas3 from type I-A CRISPR–Cas system
- Abstract
- 1: Introduction
- 2: Materials and equipment
- 3: Step-by-step method details
- 4: Applications
- 5: Conclusions
- References
- Further reading
- Chapter Fifteen: Purification and characterization of Mtr4 and TRAMP from S. cerevisiae
- Abstract
- 1: Introduction
- 2: Expression and purification of ScMtr4
- 3: Expression and purification of ScTrf4-Air2
- 4: Reconstitution of the TRAMP complex
- 5: Helicase unwinding assay
- 6: Conclusion
- References
- Chapter Sixteen: Methods to assess helicase and translocation activities of human nuclear RNA exosome and RNA adaptor complexes
- Abstract
- 1: Introduction
- 2: RNA helicase assays with MTR4 and RNA adaptor complexes
- 3: RNA unwinding and decay assays of MTR4-exosome complexes
- 4: Preparation of RNA-loaded human MTR4-exosome complex for structural studies
- Acknowledgments
- References
- Chapter Seventeen: Using hydrogen-deuterium exchange mass spectrometry to characterize Mtr4 interactions with RNA
- Abstract
- 1: Introduction
- 2: Designing an HDX-MS experiment for a protein-RNA complex
- 3: Definition of experimental parameters for HDX-MS of an RNA-protein complex
- 4: Using HDX-MS to identify molecular determinants of RNA-binding by Mtr4
- 5: Summary
- Acknowledgments
- References
- Edition: 1
- Published: August 12, 2022
- No. of pages (Hardback): 536
- No. of pages (eBook): 536
- Imprint: Academic Press
- Language: English
- Hardback ISBN: 9780323997737
- eBook ISBN: 9780323997744
MT
Michael Trakselis
Michael grew up in a western suburb of Chicago called Aurora, IL, or better known as Wayne’s World. He got his BS in Psychology and Chemistry at the University of Illinois, Urbana-Champaign. After which, he employed as a technician working on analytical method development at Abbott Laboratories. From 1998-2002 he was a PhD student at Penn State University working in Stephen Benkovic lab on the Bacteriophage T4 replisome assembly and dynamics. In 2003, he started a postdoctoral fellowship in Ron Laskey’s laboratory at the University of Cambridge/Hutchison MRC in the UK. In 2006, he started his independent career at the University of Pittsburgh Chemistry department. Starting 2014, he moved his laboratory to Baylor University, where he currently lives with his family. There, the Trakselis laboratory is currently studying aspects of DNA replication and repair spanning from the very in vitro biochemical to the very in vivo cell and human biology.
Affiliations and expertise
Associate Professor and Director of Graduate Affairs, Baylor University, TX, USARead Helicase Enzymes Part B on ScienceDirect