Cyclization of short DNA fragments and bending fluctuations of the double helix

Quan Du, Chaim Smith, Nahum Shiffeldrim, Maria Vologodskaia, Alexander Vologodskii

Research output: Contribution to journalArticle

203 Citations (Scopus)

Abstract

Cloutier and Widom [Cloutier, T. E. & Widom, J. (2004) Mol. Cell 14, 355-362] recently reported that the cyclization efficiency of short DNA fragments, about 100 bp in length, exceeds theoretical expectations by three 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. Therefore, we carefully reinvestigated the cyclization of 100-bp DNA fragments experimentally and found their cyclization efficiency to be in remarkable agreement with the traditional model of DNA bending. We also found an explanation for the discrepancy between our results and those of Cloutier and Widom.

Original languageEnglish (US)
Pages (from-to)5397-5402
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume102
Issue number15
DOIs
StatePublished - Apr 12 2005
Externally publishedYes

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Cyclization
DNA
Base Pairing

Keywords

  • DNA bending
  • DNA cyclization
  • DNA flexibility
  • DNA kinks

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Cyclization of short DNA fragments and bending fluctuations of the double helix. / Du, Quan; Smith, Chaim; Shiffeldrim, Nahum; Vologodskaia, Maria; Vologodskii, Alexander.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 15, 12.04.2005, p. 5397-5402.

Research output: Contribution to journalArticle

Du, Quan ; Smith, Chaim ; Shiffeldrim, Nahum ; Vologodskaia, Maria ; Vologodskii, Alexander. / Cyclization of short DNA fragments and bending fluctuations of the double helix. In: Proceedings of the National Academy of Sciences of the United States of America. 2005 ; Vol. 102, No. 15. pp. 5397-5402.
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