BROWSE

Related Scientist

Researcher

이오철
복잡계 자기조립 연구단
more info

Two conformational states in D-shaped DNA: Effects of local denaturation

Cited 0 time in webofscience Cited 0 time in scopus
193 Viewed 43 Downloaded
Title
Two conformational states in D-shaped DNA: Effects of local denaturation
Author(s)
O.-chul Lee; Kim C.; Kim J.-Y.; Lee N.K.; Wokyung Sung
Publication Date
2016-06
Journal
SCIENTIFIC REPORTS, v.6, no., pp.28239 -
Publisher
NATURE PUBLISHING GROUP
Abstract
The bending of double-stranded(ds) DNA on the nano-meter scale plays a key role in many cellular processes such as nucleosome packing, transcription-control, and viral-genome packing. In our recent study, a nanometer-sized dsDNA bent into a D shape was formed by hybridizing a circular single-stranded(ss) DNA and a complementary linear ssDNA. Our fluorescence resonance energy transfer (FRET) measurement of D-DNA revealed two types of conformational states: a less-bent state and a kinked state, which can transform into each other. To understand the origin of the two deformed states of D-DNA, here we study the presence of open base-pairs in the ds portion by using the breathing-DNA model to simulate the system. We provide strong evidence that the two states are due to the emergence of local denaturation, i.e., a bubble in the middle and two forks at ends of the dsDNA portion. We also study the system analytically and find that the free-energy landscape is bistable with two minima representative of the two states. The kink and fork sizes estimated by the analytical calculation are also in excellent agreement with the results of the simulation. Thus, this combined experimental-simulation-analytical study corroborates that highly bent D-DNA reduces bending stress via local denaturation.
URI
http://pr.ibs.re.kr/handle/8788114/2719
DOI
10.1038/srep28239
ISSN
2045-2322
Appears in Collections:
Center for Self-assembly and Complexity(복잡계 자기조립 연구단) > Journal Papers (저널논문)
Files in This Item:
SREP28239_성우경교수님 논문.pdfDownload

qrcode

  • facebook

    twitter

  • Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.
해당 아이템을 이메일로 공유하기 원하시면 인증을 거치시기 바랍니다.

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Browse