Localized single-stranded bubble mechanism for cyclization of short double helix DNA

Jie Yan*, John F. Marko

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

209 Scopus citations

Abstract

The localized single-stranded bubble mechanism, which was used for cyclization of short double helix DNA, was studied. It was found that double-stranded DNA molecules of approximately 100 base pairs in length have a probability of cyclization which is up to 105 times larger than that expected based on the known bending modulus of the double-helix. A detailed calculation using a transfer-matrix technique for calculation of end-to-end distances along semiflexible polymers was also analyzed. It was concluded that a realistic estimate of the energetic cost of bubble formation leads to a large enough enhancement of cyclization probability for short DNA to be a plausible explanation of the experimental data.

Original languageEnglish (US)
Article number108108
Pages (from-to)108108-1-108108-4
JournalPhysical review letters
Volume93
Issue number10
DOIs
StatePublished - Sep 3 2004

ASJC Scopus subject areas

  • Physics and Astronomy(all)

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