title: Azobenzene photoisomerization-induced destabilization of B-DNA.
abstract: Molecular photoswitches provide a promising way for selective regulation of nanoscaled biological systems. It has been shown that conformational changes of azobenzene, one of the widely used photoswitches, can be used to reversibly control DNA duplex formation. Here, we investigate the conformational response of DNA upon azobenzene binding and isomerization, using a threoninol linker that has been experimentally investigated recently. To this end, nonequilibrium molecular dynamics simulations are carried out using a switching potential describing the photoinduced isomerization. Attachment of azobenzene leads to a distortion of the DNA helical conformation that is similar for the trans and cis forms. However, the trans form is stabilized by favorable stacking interactions whereas the cis form is found to remain flipped out of the basepair-stacked position. Multiple azobenzene attachment augments the distortion in DNA helical conformation. The distorted DNA retains nativelike pairing of bases at ambient temperatures, but shows weaker basepairing compared to native DNA at an elevated temperature.
authors.affiliation: Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany. Electronic address: biswas@em.uni-frankfurt.de.
authors.forename: Mithun
authors.initials: M
authors.lastname: Biswas
authors.affiliation: Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany. Electronic address: burghardt@chemie.uni-frankfurt.de.
authors.forename: Irene
authors.initials: I
authors.lastname: Burghardt
mesh_terms: D000605:Amino Alcohols / Q000737:chemistry; D001391:Azo Compounds / Q000737:chemistry*; D002072:Butylene Glycols / Q000737:chemistry; D059371:DNA, B-Form / Q000737:chemistry*; D007536:Isomerism; D056004:Molecular Dynamics Simulation; D055668:Photochemical Processes; D013696:Temperature
chemical_list: D000605:Amino Alcohols; D001391:Azo Compounds; D002072:Butylene Glycols; D059371:DNA, B-Form; C532652:threoninol; C009850:azobenzene