International Conference on Physics.SPb/2025

A model for the equilibrium binding of the intercalating dye SYBR Green I during DNA amplification

D. R. Ibragimov^a, A. A. Fedorov^a, D. A. Varlamov<sup>b

a</sup> Institute for Analytical Instrumentation, Russian Academy of Sciences, St. Petersburg
^b All-Russia Research Institute of Agricultural Biotechnology, Moscow

Abstract: A model of the polymerase chain reaction (PCR) with a fluorescent signal generated by the intercalating dye SYBR Green I is proposed. The DNA amplification model describes the reaction kinetics occurring during the annealing and elongation stages. In the model, the fluorescence intensity is determined by the amount of bound dye, which is calculated using the dissociation constant of the equilibrium reaction between the dye and double-stranded DNA. The model demonstrated high accuracy in approximating experimental data, as well as the ability to predict the initial number of DNA molecules in the sample.

Keywords: real-time PCR model, SYBR Green I dye, Runge–Kutta methods, Nelder–Mead method.

Received: 05.05.2025
Revised: 01.07.2025
Accepted: 07.07.2025

DOI: 10.61011/PJTF.2025.24.61748.8073

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