title: DNA bending by photolyase in specific and non-specific complexes studied by atomic force microscopy.
abstract: Specific and non-specific complexes of DNA and photolyase are visualised by atomic force microscopy. As a substrate for photolyase a 1150 bp DNA restriction fragment was UV-irradiated to produce damaged sites at random positions. Comparison with a 735 bp undamaged DNA fragment made it possible to separate populations of specific and non-specific photolyase complexes on the 1150 bp fragment, relieving the need for highly defined substrates. Thus it was possible to compare DNA bending for specific and non-specific interactions. Non-specific complexes show no significant bending but increased rigidity 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.
authors.affiliation: Applied Optics Group, Department of Applied Physics, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands.
authors.forename: J
authors.initials: J
authors.lastname: van Noort
authors.forename: F
authors.initials: F
authors.lastname: Orsini
authors.forename: A
authors.initials: A
authors.lastname: Eker
authors.forename: C
authors.initials: C
authors.lastname: Wyman
authors.forename: B
authors.initials: B
authors.lastname: de Grooth
authors.forename: J
authors.initials: J
authors.lastname: Greve
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D004265:DNA Helicases; D004268:DNA-Binding Proteins / Q000235:genetics*; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000378:metabolism*; D006801:Humans; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004268:DNA-Binding Proteins; C072022:XPBC-ERCC-3 protein; D004247:DNA; D004265:DNA Helicases; D004255:Deoxyribodipyrimidine Photo-Lyase