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.
ASJC Scopus subject areas
- Physics and Astronomy(all)