Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition

Front Cover
Springer, Nov 29, 2016 - Science - 199 pages

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.

 

What people are saying - Write a review

We haven't found any reviews in the usual places.

Contents

Introduction
1
Methods
23
Integration Host Factor IHFDNA Interaction
49
Lesion Recognition by XPC Rad4 Protein
91
DNA Mismatch Repair
159
Appendix A
181
Appendix B
185
References
192
VITA
195
Copyright

Other editions - View all

Common terms and phrases

About the author (2016)

Yogambigai Velmurugu was awarded the PhD degree by the University of Illinois, Chicago, in 2015.

Bibliographic information