Effects of kink and flexible hinge defects on mechanical responses of short double stranded DNA molecules

Details Effects of kink and flexible hinge defects on mechanical responses of short double stranded DNA molecules Effects of kink and flexible hinge defects on mechanical responses of short double stranded DNA molecules

2008-02-04

arxiv.org/abs/0802.0356v2

PHYSICAL REVIEW E 77, 041907 (2008)

Biology

Quantitative Biology

Biomolecules

9 pages with 9 figures. Theoretical calculation based on transfer matrix. Minor updates, a new figure and more discussions are

Scientific paper

10.1103/PhysRevE.77.041907

We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible polymer model. The defects discussed are kinks and flexible hinges either permanently fixed on DNA or thermally excited. Their effects on extension shift, the effective persistence length, the end-to-end distance distribution, and the cyclization probability are computed using a transfer-matrix method. Our predictions will be useful in future experimental designs to study DNA nicks or mismatch base pairs, mechanics of specific DNA sequences, and specific DNA-protein interaction using magnetic tweezer, fluorescence resonance energy transfer or plasmon resonance technique, and the traditional biochemistry cyclization probability measurements.

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