DNAOD: A Predictive Tool for DNA Absorption Spectra Using A Three-Base Nearest-Neighbor Model

Quantification of DNA is a very important aspect in biological and chemical field of research. One common method for DNA quantification involves leveraging the extinction coefficient and absorbance parameters obtained from the absorption spectrum of a certain DNA sequence, with particular emphasis at the 260 nm wavelength. While methods for DNA quantification based on extinction coefficient have been reported since some time ago1, innovations in this domain have been sparse. Here, we introduce an absorption spectra prediction tool tailored for single-stranded DNA based on its extinction coefficient employing a three-sequence nearest-neighbor model. This model extends the conventional nearest-neighbor approach by considering three sequence bases instead of two, which greatly simplifies the step of calculating extinction coefficient. Our proposed model demonstrated high prediction accuracy when compared with both experimental data and predicted data using established models. To enhance accessibility, we provide a simple, user-friendly Python code for facile implementation of this model. Our findings would serve as a framework for further advances in DNA quantification, offering a valuable tool for diverse applications in molecular biology and biotechnology.