Cooperative kinking at distant sites in mechanically stressed DNA.

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Serval ID
serval:BIB_AAD051219F59
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Cooperative kinking at distant sites in mechanically stressed DNA.
Journal
Nucleic Acids Research
Author(s)
Lionberger T.A., Demurtas D., Witz G., Dorier J., Lillian T., Meyhöfer E., Stasiak A.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2011
Volume
39
Number
22
Pages
9820-9832
Language
english
Abstract
In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are capable of relieving mechanical stress within the template. DNA minicircles offer a robust model system to study stress-induced DNA structures. Using DNA minicircles on the order of 100 bp in size, we have been able to control the bending and torsional stresses within a looped DNA construct. Through a combination of cryo-EM image reconstructions, Bal31 sensitivity assays and Brownian dynamics simulations, we have been able to analyze the effects of biologically relevant underwinding-induced kinks in DNA on the overall shape of DNA minicircles. Our results indicate that strongly underwound DNA minicircles, which mimic the physical behavior of small regulatory DNA loops, minimize their free energy by undergoing sequential, cooperative kinking at two sites that are located about 180° apart along the periphery of the minicircle. This novel form of structural cooperativity in DNA demonstrates that bending strain can localize hyperflexible kinks within the DNA template, which in turn reduces the energetic cost to tightly loop DNA.
Pubmed
Web of science
Open Access
Yes
Create date
13/10/2011 10:35
Last modification date
20/08/2019 15:14
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