Using DNA looping to measure sequence dependent DNA elasticity

2012 ◽  
Author(s):  
Alan Kandinov ◽  
Krishnan Raghunathan ◽  
Jens-Christian Meiners
2012 ◽  
Vol 102 (3) ◽  
pp. 276a
Author(s):  
Tung Le ◽  
Harold Kim

2009 ◽  
Vol 96 (3) ◽  
pp. 20a
Author(s):  
David P. Wilson ◽  
J.C. Meiners ◽  
Todd Lillian ◽  
Alexei Tkachenko ◽  
Noel C. Perkins

2003 ◽  
Vol 118 (15) ◽  
pp. 7127-7140 ◽  
Author(s):  
Bernard D. Coleman ◽  
Wilma K. Olson ◽  
David Swigon

2000 ◽  
Vol 83 (3) ◽  
pp. 223-237 ◽  
Author(s):  
Ilaria Filesi ◽  
Stefano Cacchione ◽  
Pasquale De Santis ◽  
Luigi Rossetti ◽  
Maria Savino

2011 ◽  
Vol 100 (3) ◽  
pp. 75a
Author(s):  
Krishnan Raghunathan ◽  
Yih-Fan Chen ◽  
Joshua Milstein ◽  
Benjamin Juliar ◽  
Justin Blaty ◽  
...  

2021 ◽  
Vol 118 (15) ◽  
pp. e2021263118
Author(s):  
Korbinian Liebl ◽  
Martin Zacharias

The sequence-dependent structure and deformability of DNA play a major role for binding of proteins and regulation of gene expression. So far, most efforts to model DNA flexibility are based on unimodal harmonic stiffness models at base-pair resolution. However, multimodal behavior due to distinct conformational substates also contributes significantly to the conformational flexibility of DNA. Moreover, these local substates are correlated to their nearest-neighbor substates. A description for DNA elasticity which includes both multimodality and nearest-neighbor coupling has remained a challenge, which we solve by combining our multivariate harmonic approximation with an Ising model for the substates. In a series of applications to DNA fluctuations and protein–DNA complexes, we demonstrate substantial improvements over the unimodal stiffness model. Furthermore, our multivariate Ising model reveals a mechanical destabilization for adenine (A)-tracts to undergo nucleosome formation. Our approach offers a wide range of applications to determine sequence-dependent deformation energies of DNA and to investigate indirect readout contributions to protein–DNA recognition.


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