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Stretching and Bending Fluctuations of Short DNA Molecules

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Title Stretching and Bending Fluctuations of Short DNA Molecules
 
Creator PADINHATEERI, R
MENON, GI
 
Subject STRANDED-DNA
DOUBLE HELIX
FLEXIBILITY
TENSION
THERMODYNAMICS
DYNAMICS
 
Description Recent measurements of the distribution of end-to-end distance in short DNA molecules infer cooperative stretching fluctuations. The assumptions underlying the analysis can be questioned if transient, thermally induced defects producing a localized decrease in bending stiffness are present in thermal equilibrium, such as regions in which DNA melts locally (bubbles), sustains large-angle bends (kinks), or can locally transform into an alternative (S-DNA) state. We study a generalized discrete worm-like chain model for DNA, capable of describing these experiments, showing that the model yields accurate fits to available experimental data. Our results indicate that DNA bending arising from such localized defects, rather than solely stretching, can be an equal contributor to end-to-end distance fluctuations for 35-bp DNA and contributes nontrivially to such fluctuations at all scales below the persistence length. The analysis suggests that such fluctuations should exhibit a scale-dependent cooperativity, specifically relevant in determining the behavior of short chains, but which saturates rapidly to a length-independent value for longer DNA, to ensure a consistent physical description of DNA across multiple scales. Our approach provides a minimal, yet accurate, coarse-grained description of DNA at the subpersistence length scales of current experimental interest.
 
Publisher CELL PRESS
 
Date 2014-10-15T13:55:05Z
2014-10-15T13:55:05Z
2013
 
Type Article
 
Identifier BIOPHYSICAL JOURNAL, 104(2)463-471
0006-3495
1542-0086
http://dx.doi.org/10.1016/j.bpj.2012.11.3820
http://dspace.library.iitb.ac.in/jspui/handle/100/15038
 
Language en