Digital Isothermal Quantification of Nucleic Acids via Simultaneous Chemical Initiation of Recombinase Polymerase Amplification Reactions on SlipChip
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In this paper, digital quantitative detection of nucleic acids was achieved at the single-molecule level by chemical initiation of over one thousand sequence-specific, nanoliter isothermal amplification reactions in parallel. Digital polymerase chain reaction (digital PCR), a method used for quantification of nucleic acids, counts the presence or absence of amplification of individual molecules. However, it still requires temperature cycling, which is undesirable under resource-limited conditions. This makes isothermal methods for nucleic acid amplification, such as recombinase polymerase amplification (RPA), more attractive. A microfluidic digital RPA SlipChip is described here for simultaneous initiation of over one thousand nL-scale RPA reactions by adding a chemical initiator to each reaction compartment with a simple slipping step after instrument-free pipet loading. Two designs of the SlipChip, two-step slipping and one-step slipping, were validated using digital RPA. By using the digital RPA SlipChip, false-positive results from preinitiation of the RPA amplification reaction before incubation were eliminated. End point fluorescence readout was used for "yes or no" digital quantification. The performance of digital RPA in a SlipChip was validated by amplifying and counting single molecules of the target nucleic acid, methicillin-resistant Staphylococcus aureus (MRSA) genomic DNA. The digital RPA on SlipChip was also tolerant to fluctuations of the incubation temperature (37-42 °C), and its performance was comparable to digital PCR on the same SlipChip design. The digital RPA SlipChip provides a simple method to quantify nucleic acids without requiring thermal cycling or kinetic measurements, with potential applications in diagnostics and environmental monitoring under resource-limited settings. The ability to initiate thousands of chemical reactions in parallel on the nanoliter scale using solvent-resistant glass devices is likely to be useful for a broader range of applications.
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SlipChip is especially appropriate for integrated DNA-based data storage because all microdroplets can be moved simultaneously by sliding, so no valves, pumps, or tubes are required.
“As a microfluidic device for handling a large array of microdroplets, SlipChip is a platform that is especially appropriate for the development of an integrated DNA-based data storage system. All the microdroplets can be moved simultaneously on a SlipChip by simply sliding the device, so no valves, pumps, or tubes are required (54–56).”
From Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage (2021) · cites this paper as [54]
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- Authors
- Shen, F., Davydova, E. K., Du, W., Kreutz, J. E., Piepenburg, O., & Ismagilov, R. F.
- Affiliations
- University of Chicago (US)
- TwistDx (United Kingdom) (GB)
- Corresponding author
- Ismagilov, Rustem F.
- Venue
- Analytical Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2011-04-08
- Volume
- 83
- Issue
- 9
- Pages
- 3533-3540
- ISSN
- 0003-2700 (ISSN-L)
- 1520-6882
- PMC
- PMC3101872
- OpenAlex
- W2087828704
- Cited by
- 240
- References
- 54
- Citations by year
- 2026: 11 · 2025: 15 · 2024: 9 · 2023: 16 · 2022: 19 · 2021: 17 · 2020: 9 · 2019: 14 · 2018: 15 · 2017: 17 · 2016: 25 · 2015: 18 · 2014: 29 · 2013: 13 · 2012: 10
- FWCI
- 10.43
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Analytical Chemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- National Institutes of Health (DP1OD003584)
- National Institute of Biomedical Imaging and Bioengineering (R01EB012946)
- Topics
- Physical Sciences › Engineering › Biomedical Engineering › Biosensors and Analytical Detection
- Physical Sciences › Engineering › Biomedical Engineering › Microfluidic and Capillary Electrophoresis Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
- Keywords
- recombinase polymerase amplification, SlipChip, chemical initiation, single-molecule detection, methicillin-resistant Staphylococcus aureus, heat tolerance
- MeSH terms
- DNA, Bacterial, Temperature, Time Factors, Polymerase Chain Reaction, Genome, Bacterial, Recombinases, Methicillin-Resistant Staphylococcus aureus
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