Linked Life Data

10447680

Source:http://linkedlifedata.com/resource/pubmed/id/10447680

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
1999-9-21
pubmed:abstractText
We investigated the behaviour of a 15mer DNA duplex, [5'd(CAGAGTCACTGGCTC)3']. [5'd(GAGCCAG)3' + 5'd(GACTCTG)3'] which contained an adenine opposite the gap. Analysis of the NMR data showed the existence of one major species, which was in equilibrium with two minor species. Their relative concentrations varied as a function of pH with a pKa of approximately 4.5. For the major species, the duplex was globally in B conformation with the central adenine stacked in the helix. The two G.C base pairs adjacent to the central adenine were well formed and a gap was present in front of this adenine. For the minor species, major structural perturbations occurred in the centre of the duplex. At neutral pH, the central adenine was involved in a G.A mismatch with G23 adjacent to the gap. Cytosine C7 was then extrahelical and no gap was observed. Under these conditions, the major neutral species corresponded to 70% of the total and the minor species to 30%. At acidic pH, the central adenine of the minor species was protonated and was involved in a G(syn).A+(anti) mismatch. The difference is that C9 is now extrahelical and G22 is implicated in the mispair. Three-dimensional models were built to initiate molecular dynamic simulations, which were in good agreement with the NMR data. Their structural stability in terms of hydrogen bonding and their flexibility are discussed and the biological significance for the interaction with DNA polymerase is evoked.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
0014-2956
pubmed:author
pubmed:issnType
Print
pubmed:volume
264
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
120-31
pubmed:dateRevised
2007-7-23
pubmed:meshHeading
pubmed:year
1999
pubmed:articleTitle
Solution structures of a duplex containing an adenine opposite a gap (absence of one nucleotide). An NMR study and molecular dynamic simulations with explicit water molecules.
pubmed:affiliation
CEA Saclay, Département de Biologie Cellulaire et Moléculaire, Service de Biochimie et Génétique Moléculaire, Gif-sur-Yvette, France.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't