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.

Two conformational states in D-shaped DNA: Effects of local denaturation

“…3(a). The two peaks have been attributed to the two conformational states of D-shaped DNA: a kinked state with short EED (high E ) and a less-bent state with long EED (low E )18 Inserting a 3-bp mismatch in the middle of the arc, as shown in Fig. 3(b), for n 0  = 10 bp, gives a FRET efficiency E  = 0.8.…”

“…18 for the experimental details). The ds portion is bent in an arc, whereas the remaining ss portion is linearly stretched.…”

“…Unlike the previous experiment18 which used upto 5 mM Mg 2+ concentration, in this work we consider 10 mM Mg 2+ concentration, which is relevant to the biological condition in cells. Our new experiment results are shown in Fig.…”

“…The two states can dynamically interconvert between each other in milliseconds. Furthermore, the experiment18 showed that D-shaped DNA with a 3-bp size mismatch in the center of the ds portion yields a FRET signal indistinguishable from that of the short-EED state. This result suggested that local melting was responsible for the short-EED state, which arises to release the large bending stress.…”

“…Recently, we performed single-molecule experiments in which we applied alternating laser excitation fluorescence resonance energy transfer (ALEX-FRET)1920 to D-shaped DNA composed of 30 bp ds portions and ss portions of various lengths18. The FRET signal from the two dyes attached to the ds portion near both ends (see Fig.…”