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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA / analysis*
  • ErbB Receptors / genetics
  • Fluorescent Dyes
  • Genes
  • Humans
  • MicroRNAs / analysis*
  • Mutation*
  • Sensitivity and Specificity
  • Single Molecule Imaging / methods*


  • Fluorescent Dyes
  • MIRN16 microRNA, human
  • MicroRNAs
  • DNA
  • EGFR protein, human
  • ErbB Receptors