Predicting DNA hybridization kinetics from sequence

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dc.citation.firstpage91en_US
dc.citation.journalTitleNature Chemistryen_US
dc.citation.lastpage98en_US
dc.citation.volumeNumber10en_US
dc.contributor.authorZhang, Jinny X.en_US
dc.contributor.authorFang, John Z.en_US
dc.contributor.authorDuan, Weien_US
dc.contributor.authorWu, Lucia R.en_US
dc.contributor.authorZhang, Angela W.en_US
dc.contributor.authorDalchau, Neilen_US
dc.contributor.authorYordanov, Boyanen_US
dc.contributor.authorPetersen, Rasmusen_US
dc.contributor.authorPhillips, Andrewen_US
dc.contributor.authorZhang, David Yuen_US
dc.date.accessioned2019-12-11T15:44:25Zen_US
dc.date.available2019-12-11T15:44:25Zen_US
dc.date.issued2018en_US
dc.description.abstractHybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.en_US
dc.identifier.citationZhang, Jinny X., Fang, John Z., Duan, Wei, et al.. "Predicting DNA hybridization kinetics from sequence." <i>Nature Chemistry,</i> 10, (2018) Springer Nature: 91-98. https://doi.org/10.1038/nchem.2877.en_US
dc.identifier.digitalnihms908084en_US
dc.identifier.doihttps://doi.org/10.1038/nchem.2877en_US
dc.identifier.urihttps://hdl.handle.net/1911/107856en_US
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer Nature.en_US
dc.titlePredicting DNA hybridization kinetics from sequenceen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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