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Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Cyclization of Short DNA Fragments and Bending Fluctuations of the Double Helix

Cloutier and Widom [Mol. Cell 14, 355?362, (2004)] recently reported that the cyclization efficiency of short DNA fragments, about 100 bp in length, exceeds theoretical expectations by 3 orders of magnitude. In an effort to resolve this discrepancy we tried modifying the theory. We investigated how the distribution of the angles between adjacent base pairs of the double helix affects the cyclization efficiency. We found that only the incorporation of sharp kinks in the angle distribution provides the desired increase of the cyclization efficiency. We did not find a model, however, that fits all cyclization data for DNA fragments of different lengths. In order to resolve this problem we reinvestigated the cyclization of 100 bp DNA fragments experimentally. Our data showed, in sharp disagreement with Cloutier and Widom, that the cyclization efficiency for these fragments does not deviate from the theoretical prediction based on the standard wormlike chain model. We also found an explanation for the discrepancy between our data and the results reported by Cloutier and Widom.

Quan Du*
Chaim Smith
Nahum Shiffeldrim
Maria Vologodskaia
Alexander Vologodskii

Department of Chemistry
31 Washington PL, Rm1001, #44
New York University
New York, NY 10003

*Phone: (212) 992-9611
Fax (212) 260-7905
Email: QD206@nyu.edu