title: How a short double-stranded DNA bends.
abstract: A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 10(2)-10(6) than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment.
authors.affiliation: Department of Physics and POSTECH Center for Theoretical Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea.
authors.forename: Jaeoh
authors.initials: J
authors.lastname: Shin
authors.affiliation: Department of Physics and POSTECH Center for Theoretical Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea.
authors.forename: O-Chul
authors.initials: OC
authors.lastname: Lee
authors.affiliation: Department of Physics and POSTECH Center for Theoretical Physics, Pohang University of Science and Technology, Pohang 790-784, South Korea.
authors.forename: Wokyung
authors.initials: W
authors.lastname: Sung
mesh_terms: D003500:Cyclization; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004247:DNA