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Nucleic Acids Research Advance Access originally published online on May 31, 2009
Nucleic Acids Research 2009 37(14):4580-4586; doi:10.1093/nar/gkp442
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Nucleic Acids Research, 2009, Vol. 37, No. 14 4580-4586
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

The flexibility of locally melted DNA

Robert A. Forties1, Ralf Bundschuh1,2,3 and Michael G. Poirier1,2,*

1Department of Physics, 2Department of Biochemistry and 3Center for RNA Biology, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210-1117, USA

*To whom correspondence should be addressed. Tel: +1 614 247 4493; Fax: +1 614 292 7557; Email: mpoirier{at}mps.ohio-state.edu

Received April 9, 2009. Revised May 8, 2009. Accepted May 11, 2009.

Protein-bound duplex DNA is often bent or kinked. Yet, quantification of intrinsic DNA bending that might lead to such protein interactions remains enigmatic. DNA cyclization experiments have indicated that DNA may form sharp bends more easily than predicted by the established worm-like chain (WLC) model. One proposed explanation suggests that local melting of a few base pairs introduces flexible hinges. We have expanded this model to incorporate sequence and temperature dependence of the local melting, and tested it for three sequences at temperatures from 23°C to 42°C. We find that small melted bubbles are significantly more flexible than double-stranded DNA and can alter DNA flexibility at physiological temperatures. However, these bubbles are not flexible enough to explain the recently observed very sharp bends in DNA.


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