Spontaneous sharp bending of DNA: Role of melting bubbles

Chongli Yuan; Elizabeth Rhoades; Xiong Wen Lou; Lynden A. Archer

doi:10.1093/nar/gkl394

Spontaneous sharp bending of DNA: Role of melting bubbles

Chongli Yuan
, Elizabeth Rhoades
, Xiong Wen Lou
, Lynden A. Archer

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

36 Citations (Scopus)

32 Downloads (CityUHK Scholars)

Abstract

The role of centrally located and distributed base pair mismatches ('melting bubbles') on localized bending and stiffness of short dsDNA fragments is evaluated using time-dependent fluorescence lifetime measurements. Distributed melting bubbles are found to induce larger bending angles and decreased levels of stiffness in DNA than centrally located ones of comparable overall size. Our results indicate that spontaneous local opening-up of the DNA duplex could facilitate sharp bending of short DNA strands even in the absence of DNA binding proteins. We also find that the occurrence of two closely spaced melting bubbles will generally be favored when a large energetic barrier must be overcome in forming the desired bent DNA structure. © 2006 Oxford University Press.

Original language	English
Pages (from-to)	4554-4560
Journal	Nucleic acids research
Volume	34
Issue number	16
DOIs	https://doi.org/10.1093/nar/gkl394
Publication status	Published - Sept 2006
Externally published	Yes

Bibliographical note

Publication details (e.g. title, author(s), publication statuses and dates) are captured on an “AS IS” and “AS AVAILABLE” basis at the time of record harvesting from the data source. Suggestions for further amendments or supplementary information can be sent to [email protected].

Funding

We are grateful to the National Science Foundation grants DMR0551185 and CMS0510239 for supporting this study. Funding to pay the Open Access publication charges for this article was provided by DMR0551185.

Publisher's Copyright Statement

This full text is made available under CC-BY-NC 2.0 UK. https://creativecommons.org/licenses/by-nc/2.0/uk/

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abstract = "The role of centrally located and distributed base pair mismatches ('melting bubbles') on localized bending and stiffness of short dsDNA fragments is evaluated using time-dependent fluorescence lifetime measurements. Distributed melting bubbles are found to induce larger bending angles and decreased levels of stiffness in DNA than centrally located ones of comparable overall size. Our results indicate that spontaneous local opening-up of the DNA duplex could facilitate sharp bending of short DNA strands even in the absence of DNA binding proteins. We also find that the occurrence of two closely spaced melting bubbles will generally be favored when a large energetic barrier must be overcome in forming the desired bent DNA structure. {\textcopyright} 2006 Oxford University Press.",

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AU - Archer, Lynden A.

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Spontaneous sharp bending of DNA: Role of melting bubbles

Abstract

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