Linked Life Data

20116399

Source:http://linkedlifedata.com/resource/pubmed/id/20116399

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2010-4-7
pubmed:abstractText
Quantitative PCR (qPCR) using fluorescent hydrolysis probes (FH-probes; TaqMan-probes) of variable genomes, such as HIV-1, can result in underestimation of viral copy numbers due to mismatches in the FH-probe's target sequences. Therefore both target conservation and physical properties of FH-probes, such as melting temperature, baseline fluorescence and secondary structure, should be considered in design of FH-probes. Analysis of a database of 1242 near full-length HIV-1 sequences with a novel computational tool revealed that the probability of target and FH-probe identity decreases exponentially with FH-probe length. In addition, this algorithm allowed for identification of continuous sequence stretches of high conservation, from which FH-probes with global HIV-1 clade coverage could be chosen. To revise the prerequisites of physical FH-probe function, properties of 30 DNA and 21 chimeric DNA locked nucleic acid (DLNA) HIV-1 FH-probes were correlated with their performance in qPCR. This identified the presence of stable secondary structures within FH-probes and the base composition and thermal stability of the 5' proximal end as novel predictors of FH-probe performance. Thus, empirically validated novel principles of FH-probe design regarding conservation and qPCR-performance were identified, which complement and extend current rules for FH-probe design.
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
May
pubmed:issn
1879-0984
pubmed:author
pubmed:copyrightInfo
Copyright 2010 Elsevier B.V. All rights reserved.
pubmed:issnType
Electronic
pubmed:volume
165
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
151-60
pubmed:dateRevised
2011-4-14
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
Rational design of HIV-1 fluorescent hydrolysis probes considering phylogenetic variation and probe performance.
pubmed:affiliation
Division of Infectious Diseases, University Hospital Zurich, University of Zurich, Zurich, Switzerland. claudia.althaus@usz.ch
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Evaluation Studies