Continuously tunable nucleic acid hybridization probes

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dc.citation.firstpage1191en_US
dc.citation.journalTitleNature Methodsen_US
dc.citation.lastpage1196en_US
dc.citation.volumeNumber12en_US
dc.contributor.authorWu, Lucia R.en_US
dc.contributor.authorWang, J. Sherryen_US
dc.contributor.authorFang, John Z.en_US
dc.contributor.authorReiser, Emilyen_US
dc.contributor.authorPinto, Alessandroen_US
dc.contributor.authorPekker, Irenaen_US
dc.contributor.authorBoykin, Richarden_US
dc.contributor.authorNgouenet, Celineen_US
dc.contributor.authorWebster, Philippa J.en_US
dc.contributor.authorBeechem, Josephen_US
dc.contributor.authorZhang, David Yuen_US
dc.date.accessioned2017-05-12T17:10:13Zen_US
dc.date.available2017-05-12T17:10:13Zen_US
dc.date.issued2015en_US
dc.description.abstractIn silico–designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0–100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.en_US
dc.identifier.citationWu, Lucia R., Wang, J. Sherry, Fang, John Z., et al.. "Continuously tunable nucleic acid hybridization probes." <i>Nature Methods,</i> 12, (2015) Springer Nature: 1191-1196. http://dx.doi.org/10.1038/nmeth.3626.en_US
dc.identifier.doihttp://dx.doi.org/10.1038/nmeth.3626en_US
dc.identifier.urihttps://hdl.handle.net/1911/94249en_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.titleContinuously tunable nucleic acid hybridization probesen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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