Continuously tunable nucleic acid hybridization probes

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dc.citation.firstpage1191
dc.citation.journalTitleNature Methods
dc.citation.lastpage1196
dc.citation.volumeNumber12
dc.contributor.authorWu, Lucia R.
dc.contributor.authorWang, J. Sherry
dc.contributor.authorFang, John Z.
dc.contributor.authorReiser, Emily
dc.contributor.authorPinto, Alessandro
dc.contributor.authorPekker, Irena
dc.contributor.authorBoykin, Richard
dc.contributor.authorNgouenet, Celine
dc.contributor.authorWebster, Philippa J.
dc.contributor.authorBeechem, Joseph
dc.contributor.authorZhang, David Yu
dc.date.accessioned2017-05-12T17:10:13Z
dc.date.available2017-05-12T17:10:13Z
dc.date.issued2015
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.
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.
dc.identifier.doihttp://dx.doi.org/10.1038/nmeth.3626
dc.identifier.urihttps://hdl.handle.net/1911/94249
dc.language.isoeng
dc.publisherSpringer Nature
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Springer Nature.
dc.titleContinuously tunable nucleic acid hybridization probes
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpost-print
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