DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy

Specific and non-specific complexes of DNA and photolyase are visualised by atomic farce microscopy. As a substrate for photolyase a 1150 bp DNA restr iction fragment was UV-irradiated to produce damaged sites at random positi ons. Comparison with a 735 bp undamaged DNA fragment made it possible to se parate populations of specific and non-specific photolyase complexes on the 1150 bp fragment, relieving the need for highly defined substrates. Thus i t was possible to compare DNA bending for specific and non-specific interac tions. Non-specific complexes show no significant bending but increased rig idity compared to naked DNA, whereas specific complexes show DNA bending of on average 36 degrees and higher flexibility. A model obtained by docking shows that photolyase can accommodate a 36 degrees bent DNA in the vicinity of the active site.