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A stoichiometric and pseudo kinetic model of loop mediated isothermal amplification

Kaur, N and Thota, N and Toley, BJ (2020) A stoichiometric and pseudo kinetic model of loop mediated isothermal amplification. In: Computational and Structural Biotechnology Journal, 18 . pp. 2336-2346.

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Official URL: https://doi.org/10.1016/j.csbj.2020.08.020


Loop mediated isothermal amplification (LAMP) is one of the most popular isothermal DNA amplification techniques for research and commercial applications, enabling amplification of both DNA and RNA (with the assistance of reverse transcriptase). The LAMP mechanism is powered by strategic primer design and a strand displacement polymerase, generating products that fold over, creating loops. LAMP leads to generation of products of increasing length over time. These products containing multiple loops are conventionally called cauliflower structures. Existing literature on LAMP provides extremely limited understanding of progression of cascades of reactions involved in the reaction and it is believed that cauliflower structures of increasing length constitute a majority of the product formed in LAMP. This study presents a first of its kind stoichiometric and pseudo kinetic model to comprehend LAMP reactions in deeper depth by (i) classifying LAMP reaction products into uniquely identifiable categories, (ii) generating a condensed reaction network to depict millions of interconnected reactions occurring during LAMP, and (iii) elucidating the pathways for amplicon generation. Despite the inherent limitations of conventional stoichiometric modelling for polymerization type reactions (the network rapidly becomes too large and intractable), our model provides new theoretical understanding of the LAMP reaction pathway. The model shows that while longer length products are formed, it is the smaller length recycle amplicons that contribute more towards the exponential increase in the amount of double stranded DNA. Prediction of concentration of different types of LAMP amplicons will also contribute substantially towards informing design of probe-based assays. © 2020 The Author(s)

Item Type: Journal Article
Publication: Computational and Structural Biotechnology Journal
Publisher: Elsevier B.V.
Additional Information: The copyright for this article belongs to the Author(s).
Keywords: Chemical reactions; DNA; Isotherms; Kinetic parameters; Kinetic theory, Commercial applications; DNA amplification; Double stranded DNA; Exponential increase; Inherent limitations; Loop mediated isothermal amplifications; Reaction pathways; Reverse transcriptases, Product design, betaine; DNA polymerase; double stranded DNA; nucleotide; reagent, amplicon; Article; bacterial gene; hspX gene; loop mediated isothermal amplification; Mycobacterium tuberculosis; nonhuman; polymerization; prediction; priority journal; reaction analysis; stoichiometry; structure analysis
Department/Centre: Division of Mechanical Sciences > Chemical Engineering
Date Deposited: 24 Jan 2023 04:26
Last Modified: 24 Jan 2023 04:26
URI: https://eprints.iisc.ac.in/id/eprint/79293

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