Overview
- Nominated as an outstanding PhD thesis by the University of Illinois at Chicago
- Describes a novel approach combining the laser T-jump technique with unique sets of fluorescent probes to unveil previously unresolved DNA dynamics in protein-DNA binding
- Helps illuminate how a searching protein interrogates DNA deformability
- Includes supplementary material: sn.pub/extras
Part of the book series: Springer Theses (Springer Theses)
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Table of contents (5 chapters)
Keywords
About this book
Using a novel approach that combines high temporal resolution of the laser T-jump technique with unique sets of fluorescent probes, this study unveils previously unresolved DNA dynamics during search and recognition by an architectural DNA bending protein and two DNA damage recognition proteins.
Many cellular processes involve special proteins that bind to specific DNA sites with high affinity. How these proteins recognize their sites while rapidly searching amidst ~3 billion nonspecific sites in genomic DNA remains an outstanding puzzle. Structural studies show that proteins severely deform DNA at specific sites and indicate that DNA deformability is a key factor in site-specific recognition. However, the dynamics of DNA deformations have been difficult to capture, thus obscuring our understanding of recognition mechanisms.
The experiments presented in this thesis uncover, for the first time, rapid (~100-500 microseconds) DNA unwinding/bending attributed to nonspecific interrogation, prior to slower (~5-50 milliseconds) DNA kinking/bending/nucleotide-flipping during recognition. These results help illuminate how a searching protein interrogates DNA deformability and eventually “stumbles” upon its target site. Submillisecond interrogation may promote preferential stalling of the rapidly scanning protein at cognate sites, thus enabling site-recognition. Such multi-step search-interrogation-recognition processes through dynamic conformational changes may well be common to the recognition mechanisms for diverse DNA-binding proteins.
Authors and Affiliations
About the author
Yogambigai Velmurugu was awarded the PhD degree by the University of Illinois, Chicago, in 2015.
Bibliographic Information
Book Title: Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition
Authors: Yogambigai Velmurugu
Series Title: Springer Theses
DOI: https://doi.org/10.1007/978-3-319-45129-9
Publisher: Springer Cham
eBook Packages: Physics and Astronomy, Physics and Astronomy (R0)
Copyright Information: Springer International Publishing AG, part of Springer Nature 2017
Hardcover ISBN: 978-3-319-45128-2Published: 16 December 2016
Softcover ISBN: 978-3-319-83218-0Published: 04 July 2018
eBook ISBN: 978-3-319-45129-9Published: 29 November 2016
Series ISSN: 2190-5053
Series E-ISSN: 2190-5061
Edition Number: 1
Number of Pages: XXI, 199
Number of Illustrations: 7 b/w illustrations, 105 illustrations in colour
Topics: Biological and Medical Physics, Biophysics, Spectroscopy and Microscopy, Protein-Ligand Interactions