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Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Stockholm Univ, Dept Biophys & Biochem, Sci Life Lab, SE-17165 Solna, Sweden..ORCID iD: 0000-0001-7609-3301
Stockholm Univ, Dept Biophys & Biochem, Sci Life Lab, SE-17165 Solna, Sweden..
Stockholm Univ, Dept Biophys & Biochem, Sci Life Lab, SE-17165 Solna, Sweden..
Ecole Polytech Fed Lausanne, Lab Microsyst, CH-1015 Lausanne, Switzerland..
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2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 8, e59Article in journal (Refereed) Published
Abstract [en]

Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1.2 aM to 190 fM. We prove the broad applicability of our analysis platform by demonstrating 5-plex detection of as little as similar to 1 pg (similar to 300 genome copies) of pathogenic DNA with simultaneous antibiotic resistance marker detection, and the analysis of rare oncogene mutations. Our method is simpler, more cost-effective and faster than other digital analysis techniques and provides the means to implement digital analysis in any laboratory equipped with a standard fluorescent microscope.

Place, publisher, year, edition, pages
2017. Vol. 45, no 8, e59
National Category
Biochemistry and Molecular Biology Microbiology in the medical area
Identifiers
URN: urn:nbn:se:uu:diva-322522DOI: 10.1093/nar/gkw1324ISI: 000400578600004PubMedID: 28077562OAI: oai:DiVA.org:uu-322522DiVA: diva2:1098243
Funder
EU, FP7, Seventh Framework Programme, 264737Swedish Foundation for Strategic Research , SBE13-0125Swedish Research CouncilSwedish Research Council Formas, 221-2011-1692EU, Horizon 2020, 115843
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2017-05-23 Created: 2017-05-23 Last updated: 2017-05-23Bibliographically approved

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Kühnemund, MalteNilsson, Mats
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