scholarly journals Weak operator binding enhances simulated lac repressor-mediated DNA looping

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a
Author(s):  
Andrew V. Colasanti ◽  
Michael A. Grosner ◽  
Pamela J. Perez ◽  
Nicolas Clauvelin ◽  
Xiang-Jun Lu ◽  
...  
Keyword(s):  
Lac Repressor ◽  
Dna Looping ◽  
Weak Operator ◽  
Operator Binding

scholarly journals FRET and Sm-FRET Characterization of a Lac Repressor-Dna Looping Landscape

2011 ◽  
Vol 100 (3) ◽  
pp. 70a-71a
Author(s):  
Jason D. Kahn ◽  
Aaron R. Haeusler ◽  
Kathy A. Goodson ◽  
Douglas S. English
Keyword(s):  
Lac Repressor ◽  
Dna Looping

scholarly journals The Effect of HU Protein on Lac-Repressor-Mediated DNA Looping

2015 ◽  
Vol 108 (2) ◽  
pp. 74a-75a
Author(s):  
Yan Yan ◽  
Sandip Kumar ◽  
Laura Finzi ◽  
David D. Dunlap
Keyword(s):  
Lac Repressor ◽  
Dna Looping ◽  
Hu Protein

scholarly journals Investigating Classic Lac Repressor-Dna Looping Experiments Using a Computational Rod Model

2010 ◽  
Vol 98 (3) ◽  
pp. 74a
Author(s):  
Andrew D. Hirsh ◽  
Todd D. Lillian ◽  
Noel C. Perkins
Keyword(s):  
Lac Repressor ◽  
Dna Looping ◽  
Rod Model

scholarly journals Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

2008 ◽  
Vol 36 (8) ◽  
pp. 2505-2513 ◽  
Author(s):  
Davide Normanno ◽  
Francesco Vanzi ◽  
Francesco Saverio Pavone
Keyword(s):  
Single Molecule ◽  
Lac Repressor ◽  
Dna Looping ◽  
Single Molecule Manipulation

Crystal structure of lac repressor core tetramer and its implications for DNA looping

Science ◽  
1995 ◽  
Vol 268 (5218) ◽  
pp. 1721-1727 ◽  
Author(s):  
A. Friedman ◽  
T. Fischmann ◽  
T. Steitz
Keyword(s):  
Crystal Structure ◽  
Lac Repressor ◽  
Dna Looping

Electrostatics and Self-Contact in an Elastic Rod Approximation for DNA

2010 ◽  
Vol 6 (1) ◽  
Author(s):  
Todd D. Lillian ◽  
N. C. Perkins
Keyword(s):  
Electrostatic Interactions ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Elastic Rod ◽  
Storage And Retrieval ◽  
Cellular Processes ◽  
The Stability ◽  
Straight Rod

Deoxyribonucleic acid (DNA) is an essential molecule that enables the storage and retrieval of genetic information. In its role during cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elastodynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions, which are essential when considering processes that result in highly supercoiled DNA including plectonemes. Herein, we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.

Electrostatics and Self Contact in an Elastic Rod Approximation for DNA

2009 ◽  
Author(s):  
Todd D. Lillian ◽  
N. C. Perkins
Keyword(s):  
Electrostatic Interactions ◽  
Regulatory Protein ◽  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Elastic Rod ◽  
Storage And Retrieval ◽  
Cellular Processes ◽  
The Stability ◽  
Straight Rod

DNA is a life-sustaining molecule that enables the storage and retrieval of genetic information. In its role during essential cellular processes, this long flexible molecule is significantly bent and twisted. Previously, we developed an elasto-dynamic rod approximation to study DNA deformed into a loop by a gene regulatory protein (lac repressor) and predicted the energetics and topology of the loops. Although adequate for DNA looping, our model neglected electrostatic interactions which are essential when considering processes that result in highly super-coiled DNA including plectonemes. Herein we extend the rod approximation to account for electrostatic interactions and present strategies that improve computational efficiency. Our calculations for the stability for a circularly bent rod and for an initially straight rod compare favorably to existing equilibrium models. With this new capability, we are now well-positioned to study the dynamics of transcription and other dynamic processes that result in DNA supercoiling.

scholarly journals HU Protein and DNA Supercoiling Dramatically Enhance Lac-Repressor-Mediated DNA Looping

2016 ◽  
Vol 110 (3) ◽  
pp. 236a
Author(s):  
Yan Yan ◽  
Fenfei Leng ◽  
David D. Dunlap ◽  
Laura Finzi
Keyword(s):  
Dna Supercoiling ◽  
Lac Repressor ◽  
Dna Looping ◽  
Hu Protein
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