Dynamics of Inter-DNA Chain Interaction of Photoresponsive DNA

Photoresponsive DNA modified with azobenzene is an attractive design molecule for efficient photoregulation of DNA hybridization, which may be used for controlling DNA functions. Although the essential step of photocontrolling DNA is the initial isomerization of the azobenzene, the dissociation/association kinetics remain unknown. Here, the time-resolved diffusion method was used to trace the dissociation/association processes of photoresponsive DNA. Although the isomerization of azobenzene occurs in picoseconds, the dissociation of the double-stranded DNA to single-stranded DNA triggered by the trans to cis isomerization takes place ∼10(7) times slower, with a time constant of 670 μs at 200 μM. From the concentration dependence, the dissociation and association rates were determined. Furthermore, the reaction rate from the single- to double-stranded DNA after the cis to trans isomerization was measured to be 3.6 ms at 200 μM. The difference in the melting temperatures of DNA between tethered trans- and cis-azobenzene is explained by the different rate of dissociation of the double-stranded form.