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A Stoichiometric and Pseudo Kinetic Model of Loop Mediated Isothermal Amplification

preprint
submitted on 22.06.2020 and posted on 24.06.2020 by Navjot Kaur, Nikhil Thota, Bhushan Toley

Loop mediated isothermal amplification (LAMP) is one of the most popular isothermal DNA amplification techniques for research and commercial applications. 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.

Funding

Innovative Young Biotechnologist Award, DBT India, (BT/010/IYBA/2016/07)

Grand Challenges Exploration Award, Bill & Melinda Gates Foundation (OPP1182249)

Extramural research grant, SERB India (EMR/2016/006029)

History

Email Address of Submitting Author

bhushan@iisc.ac.in

Institution

Indian Institute of Science

Country

India

ORCID For Submitting Author

0000-0003-0119-2350

Declaration of Conflict of Interest

No conflict of interest

Version Notes

This is Version 1

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in Computational and Structural Biotechnology Journal

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