Dynamic Release of Bending Stress in Short Double-Stranded DNA by Two Types of Deformation

Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) for its biological functions. Local-melting in the middle of dsDNA (kink), which reduce the energy cost of bending, have been suggested as alternative DNA conformations in addition to the simple bending of dsDNA in the presence of high constrain force. However, the conformations of deformed dsDNA by high bending force and their dynamic characters remain unknown. Here, we report that the strong bending induces not only the kink in the middle of dsDNA but also the end-melting of dsDNA by applying single-molecule fluorescence resonance energy transfer (smFRET) to D-shaped DNA nanostructure consisted of dsDNA (30 bp) and single-stranded DNA (4 - 30 nt). We directly proved that two deformed structures of dsDNA are not permanent but dynamically interconverted each other in millisecond scales. The transition from end-melting to kink is dominated by entropy (anti-Arrhenius behavior), while the transition from kink to end-melting is dominated by enthalpy. The presence of the mismatch or permanent bubble in dsDNA accelerates the kink formation with less compressive force and the kink state becomes permanent when the size of permanent bubble is larger than three base pairs.