title: Backbone dynamics of DNA containing 8-oxoguanine: importance for substrate recognition by base excision repair glycosylases.
abstract: Except for the functional groups sited within the major or minor grooves, the bases of B-DNA are quite protected from the external environment. Enzymes that modify the bases often "flip out" the target into an extrahelical position before the chemistry step is carried out. Examples of this mechanism are the base excision repair glycosylases and the restriction enzyme methylases. The question arises about the mechanism of substrate recognition for these enzymes and how closely it is linked to the base flipping step. Molecular dynamics simulations (AMBER, PME electrostatics) of fully solvated, cation neutralized, DNA sequences containing 8-oxoguanine (8OG) and of appropriate normal (control) DNAs have been carried out. The dynamics trajectories were analyzed to identify those properties of the DNA structure in the vicinity of the altered base, or its dynamics, that could contribute to molecular discrimination between substrate and non-substrate DNA sites. The results predict that the FPG enzyme should flip out the cytosine base paired with the scissile 8OG, not the target base itself.
authors.affiliation: The Sealy Center for Molecular Science and Department of Human Biological Chemistry and Genetics, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-1071, USA. bdodson@scms.utmb.edu
authors.forename: M L
authors.initials: ML
authors.lastname: Dodson
authors.forename: R S
authors.initials: RS
authors.lastname: Lloyd
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004249:DNA Damage; D045647:DNA Glycosylases; D004260:DNA Repair; D006147:Guanine / Q000031:analogs & derivatives* / Q000737:chemistry*; D008956:Models, Chemical; D009699:N-Glycosyl Hydrolases / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: C024829:8-hydroxyguanine; D006147:Guanine; D004247:DNA; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; C061738:mutY adenine glycosylase