| pubmed-article:20116399 | rdf:type | pubmed:Citation | lld:pubmed |
| pubmed-article:20116399 | lifeskim:mentions | umls-concept:C0019704 | lld:lifeskim |
| pubmed-article:20116399 | lifeskim:mentions | umls-concept:C0020291 | lld:lifeskim |
| pubmed-article:20116399 | lifeskim:mentions | umls-concept:C0597198 | lld:lifeskim |
| pubmed-article:20116399 | lifeskim:mentions | umls-concept:C0205419 | lld:lifeskim |
| pubmed-article:20116399 | lifeskim:mentions | umls-concept:C0303920 | lld:lifeskim |
| pubmed-article:20116399 | lifeskim:mentions | umls-concept:C0182400 | lld:lifeskim |
| pubmed-article:20116399 | lifeskim:mentions | umls-concept:C1707689 | lld:lifeskim |
| pubmed-article:20116399 | pubmed:issue | 2 | lld:pubmed |
| pubmed-article:20116399 | pubmed:dateCreated | 2010-4-7 | lld:pubmed |
| pubmed-article:20116399 | 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. | lld:pubmed |
| pubmed-article:20116399 | pubmed:commentsCorrections | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:20116399 | pubmed:language | eng | lld:pubmed |
| pubmed-article:20116399 | pubmed:journal | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:20116399 | pubmed:citationSubset | IM | lld:pubmed |
| pubmed-article:20116399 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:20116399 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:20116399 | pubmed:chemical | http://linkedlifedata.com/r... | lld:pubmed |
| pubmed-article:20116399 | pubmed:status | MEDLINE | lld:pubmed |
| pubmed-article:20116399 | pubmed:month | May | lld:pubmed |
| pubmed-article:20116399 | pubmed:issn | 1879-0984 | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:FischerMarekM | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:JoosBedaB | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:GünthardHuldr... | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:NiederöstBarb... | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:MetznerKarin... | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:GianellaSaraS | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:RiederPhilipP | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:von... | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:KouyosRoger... | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:SchmidAdrianA | lld:pubmed |
| pubmed-article:20116399 | pubmed:author | pubmed-author:AlthausClaudi... | lld:pubmed |
| pubmed-article:20116399 | pubmed:copyrightInfo | Copyright 2010 Elsevier B.V. All rights reserved. | lld:pubmed |
| pubmed-article:20116399 | pubmed:issnType | Electronic | lld:pubmed |
| pubmed-article:20116399 | pubmed:volume | 165 | lld:pubmed |
| pubmed-article:20116399 | pubmed:owner | NLM | lld:pubmed |
| pubmed-article:20116399 | pubmed:authorsComplete | Y | lld:pubmed |
| pubmed-article:20116399 | pubmed:pagination | 151-60 | lld:pubmed |
| pubmed-article:20116399 | pubmed:dateRevised | 2011-4-14 | lld:pubmed |
| pubmed-article:20116399 | pubmed:meshHeading | pubmed-meshheading:20116399... | lld:pubmed |
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| pubmed-article:20116399 | pubmed:meshHeading | pubmed-meshheading:20116399... | lld:pubmed |
| pubmed-article:20116399 | pubmed:year | 2010 | lld:pubmed |
| pubmed-article:20116399 | pubmed:articleTitle | Rational design of HIV-1 fluorescent hydrolysis probes considering phylogenetic variation and probe performance. | lld:pubmed |
| pubmed-article:20116399 | pubmed:affiliation | Division of Infectious Diseases, University Hospital Zurich, University of Zurich, Zurich, Switzerland. claudia.althaus@usz.ch | lld:pubmed |
| pubmed-article:20116399 | pubmed:publicationType | Journal Article | lld:pubmed |
| pubmed-article:20116399 | pubmed:publicationType | Research Support, Non-U.S. Gov't | lld:pubmed |
| pubmed-article:20116399 | pubmed:publicationType | Evaluation Studies | lld:pubmed |
