title: Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.
abstract: Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using D-shaped DNA nanostructures. The two types of deformed dsDNA structures dynamically interconvert on a millisecond timescale. The transition from a fork to a kink is dominated by entropic contribution (anti-Arrhenius behavior), while the transition from a kink to a fork is dominated by enthalpic contributions. The presence of mismatches in dsDNA accelerates kink formation, and the transition from a kink to a fork is removed when the mismatch size is three base pairs.
authors.affiliation: Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea).
authors.forename: Cheolhee
authors.initials: C
authors.lastname: Kim
authors.affiliation: Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea).
authors.forename: O-chul
authors.initials: OC
authors.lastname: Lee
authors.affiliation: Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea).
authors.forename: Jae-Yeol
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea).|IBS Center for Self-assembly and Complexity, Pohang 790-784 (Republic of Korea).
authors.forename: Wokyung
authors.initials: W
authors.lastname: Sung
authors.affiliation: Department of Physics, Pohang University of Science and Technology, Pohang 790-784 (Republic of Korea). nklee@postech.ac.kr.
authors.forename: Nam Ki
authors.initials: NK
authors.lastname: Lee
mesh_terms: D020137:Base Pair Mismatch / Q000235:genetics*; D004247:DNA / Q000737:chemistry; D008958:Models, Molecular
chemical_list: D004247:DNA
keywords: DNA structures; FRET; bending; kinks; mismatched sequences