Mathematical Modeling of DNA Yield Using Box-Behnken Design for Key Extraction Parameters: Box-Behnken Design for Optimizing DNA Extraction Yield

Rashid Saif; Saeeda Zia; Farwa Afzal

doi:10.54393/fbt.v5i2.174

Authors

Rashid Saif Department of Biotechnology, Qarshi University, Lahore, Pakistan
Saeeda Zia Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Foundation for Advancement of Science and Technology, Lahore, Pakistan
Farwa Afzal Department of Sciences and Humanities, National University of Computer and Emerging Sciences, Foundation for Advancement of Science and Technology, Lahore, Pakistan

DOI:

https://doi.org/10.54393/fbt.v5i2.174

Keywords:

DNA Yield Modeling, Response Surface Design, Mathematical Biology, Biomathematical Modeling

Abstract

The current research was intrigued to explore an enzyme-assisted inorganic salt-based DNA extraction protocol to obtain maximum yield from peripheral whole blood samples. Objectives: To develop an integrated model that synthesizes principles from chemistry, biology, statistics, and mathematics to optimize key parameters. Methods: This study used Box-Behnken Design (BBD) to model and simulate the extraction process with three factors and three levels each, which is one of the widely used functional approaches of response surface methodology (RSM). Key extraction parameters were considered, such as incubation temperature (54, 56, 58°C), time (8, 10, 12 hrs.), and proteinase K enzyme concentrations (8, 10, 12 µL). With this selected design, RSM entails a mathematical model with experimental data to optimize DNA yield. Results: The best fit simulation settings yielded the maximum DNA at an incubation temperature of 56°C for 10 hours with a proteinase K enzyme volume of 10µL. Utilizing these parameters, a yield of 300ng/µL was obtained. A confirmation run under these settings validated the prediction, with observed yields closely matching the model's estimates (p>0.05), indicating strong agreement between the model and experimental outcomes. Conclusions: In conclusion, other DNA extraction variables may also be applied for a more robust model for obtaining the maximum DNA yield from minimal specimens/reagents, particularly in forensic investigations.

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