DNA Bending Force Facilitates Z-DNA Formation under Physiological Salt Conditions

Z-DNA, a noncanonical helical structure of double stranded DNA (dsDNA), plays pivotal roles in various biological processes, including transcription regulation. Mechanical stresses on dsDNA, such as twisting and stretching, help to form Z-DNA. However, the effect of DNA bending, one of the most common dsDNA deformations, on Z-DNA formation is utterly unknown. Here, we show that DNA bending induces the formation of Z DNA, that is, more Z-DNA is formed as the bending force becomes stronger. We regulated the bending force on dsDNA by using D shaped DNA nanostructures. The B-Z transition was observed by single-molecule fluorescence resonance energy transfer. We found that as the bending force became stronger, Z-DNA was formed at lower Mg2+ concentrations. When dsDNA contained cytosine methylations, the B-Z transition occurred at 78 mM Mg2+ (midpoint) in the absence of the bending force. However, the B-Z transition occurred at a 28-fold lower Mg2+ concentration (2.8 mM) in the presence of the bending force. Monte Carlo simulation suggested that the B-Z transition stabilizes the bent form via the formation of the B-Z junction with base extrusion, which effectively releases the bending stress on DNA. Our results clearly show that the bending force facilitates the B-Z transition under physiological salt conditions.

Automated summary

This study reveals that DNA bending force facilitates the formation of Z-DNA, and increasing bending force leads to more Z-DNA formation. The bending force affects the Mg2+ concentration threshold for B-Z transition, lowering it. Monte Carlo simulations suggest that the B-Z transition stabilizes the bent DNA conformation through the formation of B-Z junction.