Using Explainable Artificial Intelligence and Molecular Dynamics to Investigate Sequence Dependent Fluorescence in Single Stranded DNA

The intensity of a photon released from cyanine dye on a labeled oligonucleotide is heavily influenced by the adjacent sequence. This phenomenon could have profound effects in biotechnologies that rely on fluorescently labeled DNA based materials such as PCR, DNA-PAINT, and FISH. For instance, the selection of a DNA probe could result in a lower Signal-to-Noise ratio necessitating further data processing procedures. Currently, π- π stacking between the cyanine dye and the terminal nucleotide is