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Methods. 2019 Jan 15;153:3-12. doi: 10.1016/j.ymeth.2018.08.002. Epub 2018 Aug 10.

A guide to nucleic acid detection by single-molecule kinetic fingerprinting.

Author information

1
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA; Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
2
Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
3
Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
4
Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. Electronic address: nwalter@umich.edu.

Abstract

Conventional methods for detecting small quantities of nucleic acids require amplification by the polymerase chain reaction (PCR), which necessitates prior purification and introduces copying errors. While amplification-free methods do not have these shortcomings, they are generally orders of magnitude less sensitive and specific than PCR-based methods. In this review, we provide a practical guide to a novel amplification-free method, single-molecule recognition through equilibrium Poisson sampling (SiMREPS), that provides both single-molecule sensitivity and single-base selectivity by monitoring the repetitive interactions of fluorescent probes to immobilized targets. We demonstrate how this kinetic fingerprinting filters out background arising from the inevitable nonspecific binding of probes, yielding virtually zero background signal. As practical applications of this digital detection methodology, we present the quantification of microRNA miR-16 and the detection of the mutation EGFR L858R with an apparent single-base discrimination factor of over 3 million.

KEYWORDS:

Amplification-free; DNA; Kinetic fingerprinting; MicroRNA; Mutation; Single-molecule fluorescence microscopy

PMID:
30099084
PMCID:
PMC6325009
[Available on 2020-01-15]
DOI:
10.1016/j.ymeth.2018.08.002
[Indexed for MEDLINE]

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