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복잡계 자기조립 연구단
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How a short double-stranded DNA bends

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Title
How a short double-stranded DNA bends
Author(s)
Shin, J; Lee, OC; Wokyung Sung
Publication Date
2015-04
Journal
JOURNAL OF CHEMICAL PHYSICS, v.142, no.15, pp.155101 -
Publisher
AMER INST PHYSICS
Abstract
A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 10(2)-10(6) than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment. (C) 2015 AIP Publishing LLC
URI
https://pr.ibs.re.kr/handle/8788114/1629
ISSN
0021-9606
Appears in Collections:
Center for Self-assembly and Complexity(복잡계 자기조립 연구단) > Journal Papers (저널논문)
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