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Nucleic Acid Quantification with Amplicon Yield in Recombinase Polymerase Amplification

Valloly, P and Roy, R (2022) Nucleic Acid Quantification with Amplicon Yield in Recombinase Polymerase Amplification. In: Analytical Chemistry, 94 (40). pp. 13897-13905.

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Official URL: https://doi.org/10.1021/acs.analchem.2c02810


Amplification-based quantitative polymerase chain reaction (qPCR) provides accurate and sensitive nucleic acid quantification. However, the requirement of temperature cycling and real-time monitoring limits its translation to many settings. Quantitative isothermal amplification methods alleviate the need for thermal cyclers; however, they still require continuous monitoring of the nucleic acid amplification on sophisticated readers. Here, we adapted an isothermal recombinase polymerase amplification (RPA) reaction to develop a semiquantitative method that relies on the final amplicon yield to estimate the initial target nucleic acid copy number. To achieve this, we developed a phenomenological model that captures the essential RPA dynamics. We identified reaction conditions that constrained the reaction yield corresponding to the starting DNA template concentration. We validated these predictions experimentally and showed that the amplicon yields at the end of the RPA reaction correlated well with the starting DNA concentration while reducing nonspecific amplification robustly. We demonstrate this approach, termed quantitative endpoint RPA (qeRPA), to detect DNA over five log orders with a detection limit of 100 molecules. Using a linear regression model of the normalized endpoint intensity (NEI) standard curve, we estimate the viral load from the serum of dengue virus-infected patients with comparable performance to qPCR. Unlike the conventional isothermal quantitative methods, qeRPA can be employed for robust and sensitive nucleic acid estimation at close to room temperature without real-time monitoring and can be beneficial for field deployment in resource-limited settings.

Item Type: Journal Article
Publication: Analytical Chemistry
Publisher: American Chemical Society
Additional Information: The copyright for this article belongs to the Author(s).
Keywords: Biomolecules; DNA; Isotherms; Linear regression; Polymerase chain reaction, Amplicons; Continuous monitoring; Cycling time; Isothermal amplifications; Nucleic acids amplification; Quantitative polymerase chain reaction; Real time monitoring; Recombinases; Temperature cycling; Thermal-cycler, Viruses
Department/Centre: Division of Interdisciplinary Sciences > Centre for Biosystems Science and Engineering
Division of Mechanical Sciences > Chemical Engineering
Date Deposited: 31 Oct 2022 10:55
Last Modified: 31 Oct 2022 10:55
URI: https://eprints.iisc.ac.in/id/eprint/77681

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