Linked Life Data

11738936

Source:http://linkedlifedata.com/resource/pubmed/id/11738936

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3-4
pubmed:dateCreated
2001-12-12
pubmed:abstractText
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.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Dec
pubmed:issn
0027-5107
pubmed:author
pubmed:issnType
Print
pubmed:day
19
pubmed:volume
487
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
93-108
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2001
pubmed:articleTitle
Backbone dynamics of DNA containing 8-oxoguanine: importance for substrate recognition by base excision repair glycosylases.
pubmed: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
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S.