Linked Life Data

14717593

Source:http://linkedlifedata.com/resource/pubmed/id/14717593

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2004-1-13
pubmed:abstractText
Despite the nontemplating nature of the abasic site, dAMP is often preferentially inserted opposite the lesion, a phenomenon commonly referred to as the "A-rule". We have evaluated the molecular mechanism accounting for this unique behavior using a thorough kinetic approach to evaluate polymerization efficiency during translesion DNA replication. Using the bacteriophage T4 DNA polymerase, we have measured the insertion of a series of modified nucleotides and have demonstrated that increasing the size of the nucleobase does not correlate with increased insertion efficiency opposite an abasic site. One analogue, 5-nitroindolyl-2'-deoxyriboside triphosphate, was unique as it was inserted opposite the lesion with approximately 1000-fold greater efficiency compared to that for dAMP insertion. Pre-steady-state kinetic measurements yield a kpol value of 126 s(-1) and a Kd value of 18 microM for the insertion of 5-nitroindolyl-2'-deoxyriboside triphosphate opposite the abasic site. These values rival those associated with the enzymatic formation of a natural Watson-Crick base pair. These results not only reiterate that hydrogen bonding is not necessary for nucleotide insertion but also indicate that the base-stacking and/or desolvation capabilities of the incoming nucleobase may indeed play the predominant role in generating efficient DNA polymerization. A model accounting for the increase in catalytic efficiency of this unique nucleobase is provided and invokes pi-pi stacking interactions of the aromatic moiety of the incoming nucleobase with aromatic amino acids present in the polymerase's active site. Finally, differences in the rate of 5-nitroindolyl-2'-deoxyriboside triphosphate insertion opposite an abasic site are measured between the bacteriophage T4 DNA polymerase and the Klenow fragment. These kinetic differences are interpreted with regard to the differences in various structural components between the two enzymes and are consistent with the proposed model for DNA polymerization.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
http://linkedlifedata.com/resource/pubmed/chemical/2'-deoxy-5'-adenosine monophosphate, http://linkedlifedata.com/resource/pubmed/chemical/2'-deoxyadenosine triphosphate, http://linkedlifedata.com/resource/pubmed/chemical/DNA Polymerase I, http://linkedlifedata.com/resource/pubmed/chemical/DNA-Directed DNA Polymerase, http://linkedlifedata.com/resource/pubmed/chemical/Deoxyadenine Nucleotides, http://linkedlifedata.com/resource/pubmed/chemical/Deoxyguanine Nucleotides, http://linkedlifedata.com/resource/pubmed/chemical/Deoxyribonucleotides, http://linkedlifedata.com/resource/pubmed/chemical/Inosine Monophosphate, http://linkedlifedata.com/resource/pubmed/chemical/Nucleic Acid Heteroduplexes, http://linkedlifedata.com/resource/pubmed/chemical/Viral Proteins, http://linkedlifedata.com/resource/pubmed/chemical/deoxyguanosine triphosphate, http://linkedlifedata.com/resource/pubmed/chemical/gene 43 protein, Enterobacteria...
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
0006-2960
pubmed:author
pubmed:issnType
Print
pubmed:day
20
pubmed:volume
43
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
393-404
pubmed:dateRevised
2010-11-18
pubmed:meshHeading
pubmed:year
2004
pubmed:articleTitle
Evaluating the contribution of base stacking during translesion DNA replication.
pubmed:affiliation
Department of Pharmacology and the Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, Non-U.S. Gov't