Nucleic Acids Research Advance Access originally published online on September 5, 2006
Nucleic Acids Research 2006 34(16):4554-4560; doi:10.1093/nar/gkl394
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Nucleic Acids Research, 2006, Vol. 34, No. 16 4554-4560
© 2006 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 |
Spontaneous sharp bending of DNA: role of melting bubbles
School of Chemical and Biomolecular Engineering, Cornell University Ithaca, NY 14853, USA 1 Department of Applied and Engineering Physics, Cornell University Ithaca, NY 14853, USA
*To whom correspondence should be addressed at School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853, USA. Tel: +1 607 254 8825; Fax: +1 607 255 9166; Email: laa25{at}cornell.edu
Received March 8, 2006. Revised May 5, 2006. Accepted May 9, 2006.
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.
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