| DOI | Resolve DOI: https://doi.org/10.2174/1574893611666161008194920 |
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| Author | Search for: Tulpan, Dan1; Search for: Montemanni, Roberto; Search for: Smith, Derek |
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| Affiliation | - National Research Council of Canada. Information and Communication Technologies
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| Format | Text, Article |
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| Subject | DNA sequence; GC-content; hybridization; melting temperature; oligonucleotides; Pearson correlation |
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| Abstract | In 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. |
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| Publication date | 2016-10-08 |
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| Publisher | Bentham Science Publishers |
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| In | |
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| Language | English |
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| Peer reviewed | Yes |
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| NPARC number | 23000906 |
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| Export citation | Export as RIS |
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| Report a correction | Report a correction (opens in a new tab) |
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| Record identifier | 0037cd72-54d5-491a-bad7-c846239c75ee |
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| Record created | 2016-11-09 |
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| Record modified | 2020-03-16 |
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