Positive feedback drives a secondary nonlinear product burst during a biphasic DNA amplification reaction

Özay, Burcu; Murphy, Shannon Danielle; Stopps, Esther Emelia; Gedeon, Tomáš; McCalla, Stephanie E.

doi:10.1039/d2an01067d

Cited by 1 publication

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References 34 publications

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“…Isothermal amplification commonly exhibits a double sigmoid curve profile, even with reactions that have a single target. This possibly happens because of secondary feedback loops which are present in some kinds of isothermal reactions 36 , though none have been reported for LAMP reactions specifically. This is visible in both fluorescent and colorimetric reporter chemistries when the target nucleic acid initial concentration is high enough (about 3 orders of magnitude higher than the Limit of Detection).…”

Section: Resultsmentioning

confidence: 99%

Data treatment methods for real-time colorimetric loop-mediated isothermal amplification reactions

Kim,

Imamura,

Winkert Raddatz

et al. 2023

Sci Rep

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With the SARS-CoV-2 pandemic and the need for affordable and rapid mass testing, colorimetric isothermal amplification reactions such as Loop-Mediated Isothermal Amplification (LAMP) are quickly rising in importance. The technique generates data that is similar to quantitative Polymerase Chain Reaction (qPCR), but instead of an endpoint color visualization, it is possible to construct a signal over a time curve. As the number of works using time-course analysis of isothermal reactions increases, there is a need to analyze data and standardize their related treatments quantitatively. Here, we take a step forward toward this goal by evaluating different available data treatments (curve models) for amplification curves, which allows for a cycle threshold-like parameter extraction. In this study, we uncover evidence of a double sigmoid equation as the most adequate model to describe amplification data from our remote diagnostics system and discuss possibilities for similar setups. We also demonstrate the use of multimodal Gompertz regression models. Thus, this work provides advances toward standardized and unbiased data reporting of Reverse Transcription (RT) LAMP reactions, which may facilitate and quicken assay interpretation, potentially enabling the application of machine learning techniques for further optimization and classification.

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Section: Resultsmentioning

confidence: 99%

Data treatment methods for real-time colorimetric loop-mediated isothermal amplification reactions

Kim,

Imamura,

Winkert Raddatz

et al. 2023

Sci Rep

View full text Add to dashboard Cite

show abstract

Positive feedback drives a secondary nonlinear product burst during a biphasic DNA amplification reaction

Abstract: Isothermal DNA amplification reactions are used in a broad variety of applications, from diagnostic assays to DNA circuits, with greater speed and less complexity than established PCR technologies. We recently...

Cited by 1 publication

References 34 publications

Data treatment methods for real-time colorimetric loop-mediated isothermal amplification reactions

Data treatment methods for real-time colorimetric loop-mediated isothermal amplification reactions

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