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 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.
van Noort
J
J
Applied Optics Group, Department of Applied Physics, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands.
Orsini
F
F
Eker
A
A
Wyman
C
C
de Grooth
B
B
Greve
J
J
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
D004268:DNA-Binding Proteins; C072022:XPBC-ERCC-3 protein; D004247:DNA; D004265:DNA Helicases; D004255:Deoxyribodipyrimidine Photo-Lyase