Kinetic Fingerprinting to Identify and Count Single Nucleic Acids

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2015 Jun 23

PMID 26098451

Citations 49

Authors

Alexander Johnson-Buck

Xin Su

Maria D Giraldez

Meiping Zhao

Muneesh Tewari

Nils G Walter

Affiliations

Soon will be listed here.

Abstract

MicroRNAs (miRNAs) have emerged as promising diagnostic biomarkers. We introduce a kinetic fingerprinting approach called single-molecule recognition through equilibrium Poisson sampling (SiMREPS) for the amplification-free counting of single unlabeled miRNA molecules, which circumvents thermodynamic limits of specificity and virtually eliminates false positives. We demonstrate high-confidence, single-molecule detection of synthetic and endogenous miRNAs in both buffer and minimally treated biofluids, as well as >500-fold discrimination between single nucleotide polymorphisms.

Citing Articles

Chromato-kinetic fingerprinting enables multiomic digital counting of single disease biomarker molecules.

Banerjee P, Ray S, Dai L, Sandford E, Chatterjee T, Mandal S bioRxiv. 2025; .

PMID: 39975368 PMC: 11838488. DOI: 10.1101/2025.01.31.636009.

How Highly Heterogeneous Sensors with Single-Molecule Resolution can Result in Robust Continuous Monitoring Over Long Time Spans.

Vu C, Yan J, de Jong A, Prins M Adv Sci (Weinh). 2024; 12(7):e2412181.

PMID: 39716982 PMC: 11831471. DOI: 10.1002/advs.202412181.

Ultrasensitive Amplification-Free Quantification of a Methyl CpG-Rich Cancer Biomarker by Single-Molecule Kinetic Fingerprinting.

Dai L, Johnson-Buck A, Laird P, Tewari M, Walter N Anal Chem. 2024; 96(43):17209-17216.

PMID: 39425638 PMC: 11648273. DOI: 10.1021/acs.analchem.4c03002.

Foundation model for efficient biological discovery in single-molecule data.

Li J, Zhang L, Johnson-Buck A, Walter N bioRxiv. 2024; .

PMID: 39253410 PMC: 11383305. DOI: 10.1101/2024.08.26.609721.

Single-Walled Carbon Nanotube Sensor Selection for the Detection of MicroRNA Biomarkers for Acute Myocardial Infarction as a Case Study.

Hendler-Neumark A, Wulf V, Bisker G ACS Sens. 2023; 8(10):3713-3722.

PMID: 37700465 PMC: 10616859. DOI: 10.1021/acssensors.3c00633.

References

Russo F, Di Bella S, Nigita G, Macca V, Lagana A, Giugno R . miRandola: extracellular circulating microRNAs database. PLoS One. 2012; 7(10):e47786. PMC: 3477145. DOI: 10.1371/journal.pone.0047786. View

Cisse I, Kim H, Ha T . A rule of seven in Watson-Crick base-pairing of mismatched sequences. Nat Struct Mol Biol. 2012; 19(6):623-7. PMC: 3372693. DOI: 10.1038/nsmb.2294. View

Zhang D, Chen S, Yin P . Optimizing the specificity of nucleic acid hybridization. Nat Chem. 2012; 4(3):208-14. PMC: 4238961. DOI: 10.1038/nchem.1246. View

Schwarzenbach H, Hoon D, Pantel K . Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011; 11(6):426-37. DOI: 10.1038/nrc3066. View

Jungmann R, Steinhauer C, Scheible M, Kuzyk A, Tinnefeld P, Simmel F . Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 2010; 10(11):4756-61. DOI: 10.1021/nl103427w. View

Sorgenfrei S, Chiu C, Gonzalez Jr R, Yu Y, Kim P, Nuckolls C . Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube field-effect transistor. Nat Nanotechnol. 2011; 6(2):126-32. PMC: 3783941. DOI: 10.1038/nnano.2010.275. View

Li L, Li X, Li L, Wang J, Jin W . Ultra-sensitive DNA assay based on single-molecule detection coupled with fluorescent quantum dot-labeling and its application to determination of messenger RNA. Anal Chim Acta. 2010; 685(1):52-7. DOI: 10.1016/j.aca.2010.11.012. View

Michelotti N, de Silva C, Johnson-Buck A, Manzo A, Walter N . A bird's eye view tracking slow nanometer-scale movements of single molecular nano-assemblies. Methods Enzymol. 2010; 475:121-48. PMC: 3013281. DOI: 10.1016/S0076-6879(10)75006-0. View

Abelson J, Blanco M, Ditzler M, Fuller F, Aravamudhan P, Wood M . Conformational dynamics of single pre-mRNA molecules during in vitro splicing. Nat Struct Mol Biol. 2010; 17(4):504-12. PMC: 2881217. DOI: 10.1038/nsmb.1767. View

10.

Ruepp A, Kowarsch A, Schmidl D, Buggenthin F, Brauner B, Dunger I . PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 2010; 11(1):R6. PMC: 2847718. DOI: 10.1186/gb-2010-11-1-r6. View

11.

Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W . An analysis of human microRNA and disease associations. PLoS One. 2008; 3(10):e3420. PMC: 2559869. DOI: 10.1371/journal.pone.0003420. View

12.

Mitchell P, Parkin R, Kroh E, Fritz B, Wyman S, Pogosova-Agadjanyan E . Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A. 2008; 105(30):10513-8. PMC: 2492472. DOI: 10.1073/pnas.0804549105. View

13.

Walter N, Huang C, Manzo A, Sobhy M . Do-it-yourself guide: how to use the modern single-molecule toolkit. Nat Methods. 2008; 5(6):475-89. PMC: 2574008. DOI: 10.1038/nmeth.1215. View

14.

Geiss G, Bumgarner R, Birditt B, Dahl T, Dowidar N, Dunaway D . Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol. 2008; 26(3):317-25. DOI: 10.1038/nbt1385. View

15.

Aitken C, Marshall R, Puglisi J . An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys J. 2007; 94(5):1826-35. PMC: 2242739. DOI: 10.1529/biophysj.107.117689. View

16.

Gunnarsson A, Jonsson P, Marie R, Tegenfeldt J, Hook F . Single-molecule detection and mismatch discrimination of unlabeled DNA targets. Nano Lett. 2007; 8(1):183-8. DOI: 10.1021/nl072401j. View

17.

Axelrod D, Burghardt T, Thompson N . Total internal reflection fluorescence. Annu Rev Biophys Bioeng. 1984; 13:247-68. DOI: 10.1146/annurev.bb.13.060184.001335. View

18.

Baaske M, Foreman M, Vollmer F . Single-molecule nucleic acid interactions monitored on a label-free microcavity biosensor platform. Nat Nanotechnol. 2014; 9(11):933-9. DOI: 10.1038/nnano.2014.180. View

19.

Ho S, Chan H, Ha A, Wong R, Li H . Direct quantification of circulating miRNAs in different stages of nasopharyngeal cancerous serum samples in single molecule level with total internal reflection fluorescence microscopy. Anal Chem. 2014; 86(19):9880-6. DOI: 10.1021/ac5025182. View

20.

Garcia-Schwarz G, Santiago J . Rapid high-specificity microRNA detection using a two-stage isotachophoresis assay. Angew Chem Int Ed Engl. 2013; 52(44):11534-7. DOI: 10.1002/anie.201305875. View