Linked Life Data

17118144

Source:http://linkedlifedata.com/resource/pubmed/id/17118144

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:dateCreated
2010-1-19
pubmed:abstractText
BACKGROUND: Channel current feature extraction methods, using Hidden Markov Models (HMMs) have been designed for tracking individual-molecule conformational changes. This information is derived from observation of changes in ionic channel current blockade "signal" upon that molecule's interaction with (and occlusion of) a single nanometer-scale channel in a "nanopore detector". In effect, a nanopore detector transduces single molecule events into channel current blockades. HMM analysis tools described are used to help systematically explore DNA dinucleotide flexibility, with particular focus on HIV's highly conserved (and highly flexible/reactive) viral DNA termini. One of the most critical stages in HIV's attack is the binding between viral DNA and the retroviral integrase, which is influenced by the dynamic-coupling induced high flexibility of a CA/TG dinucleotide positioned precisely two base-pairs from the blunt terminus of the duplex viral DNA. This suggests the study of a family of such CA/TG dinucleotide molecules via nanopore measurement and cheminformatics analysis. RESULTS: HMMs are used for level identification on the current blockades, HMM/EM with boosted variance emissions are used for level projection pre-processing, and time-domain FSAs are used to parse the level-projected waveform for kinetic information. The observed state kinetics of the DNA hairpins containing the CA/TG dinucleotide provides clear evidence for HIV's selection of a peculiarly flexible/interactive DNA terminus.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-10024440, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-10585944, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-10623509, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-10623510, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-10639130, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-10936653, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-11231558, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-11406377, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-11513580, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-12146955, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-12547778, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-12582251, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-12717729, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-12815257, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-12842466, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-1406328, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-15585125, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-15870206, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-1702543, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-17118135, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-17118147, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-2167180, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-2908426, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-3351923, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-3357884, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-3413094, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-3670410, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-4028161, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-6273591, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-7154084, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-7338904, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-7604014, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-7752887, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-7831800, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-8363924, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-8640526, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-8648652, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-8943190, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-8995657, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-9030689, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-9126841, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-9405150, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-9465037, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-9622486, http://linkedlifedata.com/resource/pubmed/commentcorrection/17118144-9836580
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1471-2105
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
7 Suppl 2
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
S22
pubmed:dateRevised
2010-9-15
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Cheminformatics methods for novel nanopore analysis of HIV DNA termini.
pubmed:affiliation
Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA. winters@cs.uno.edu
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural