DNA bending facilitates the formation of Z-DNA investigated by single-molecule FRET.

Abstract

Z-DNA, a noncanonical helical structure of double-stranded DNA (dsDNA), plays essential roles in diverse biological processes such as transcription regulation. Mechanical stresses on dsDNA, such as torsion and tension, could form Z-DNA more easily. However, the effect of DNA bending, one of the most common deformations of DNA, on Z-DNA formation is utterly elusive. Herein, we show that DNA bending facilitates the formation of Z-DNA, that is, Z-DNA is formed at lower Mg2+ concentration as the bending force becomes stronger. We regulated the bending force on dsDNA via D-shaped DNA nanostructures and observed the B-Z transition by single-molecule FRET. In the presence of the bending force, the B-Z transition of methylated DNA occurred at a 28-fold lower Mg2+ condition (2.8 mM) which is in the range of physiological salt concentrations. Monte Carlo simulation suggested that the base extrusion at the B-Z junction according to the B-Z transition may stabilize the Z-DNA form via releasing the bending stress on dsDNA. Our results certainly show that DNA bending force induces the formation of Z-DNA and provide a new insight into the effect of DNA bending.