Correlations between experimentally-determined melting temperatures and GC-content for short DNA strands

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DOIResolve DOI: http://doi.org/10.2174/1574893611666161008194920
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TypeArticle
Journal titleCurrent Bioinformatics
ISSN1574-8936
Volume11
Issue999
Pages11
SubjectDNA sequence; GC-content; hybridization; melting temperature; oligonucleotides; Pearson correlation
AbstractIn many bioinformatics applications DNA duplex hybridization is traditionally estimated using GC-content and melting temperature calculations based on the sequence base composition. Here we show that GC-content is a far from perfect predictor of DNA strand hybridization strength compared to experimentally-determined melting temperatures. We built a manually curated set of 373 experimental data points collected from 21 publications, each point representing a DNA strand with length between 4 and 35 nucleotides and its corresponding experimentally determined melting temperature measured under specific sequence and salt concentrations. For each data point we calculated the corresponding GC-content and we separated the set into 12 subsets to minimize the variability of experimental conditions. Based on calculated Pearson product-moment correlation coefficients we conclude that GC-content only seldom correlates well with experimentally determined melting temperatures and thus it is not a strictly necessary constraint when used to control the uniformity of DNA strands.
Publication date
PublisherBentham Science Publishers
LanguageEnglish
AffiliationNational Research Council Canada; Information and Communication Technologies
Peer reviewedYes
NPARC number23000906
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Record identifier0037cd72-54d5-491a-bad7-c846239c75ee
Record created2016-11-09
Record modified2016-11-09
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