Computational design of synthetic fluorescent nucleotides: tuning electron transfer and fluorescence competition with functionalization location of perylene tag

Synthetic fluorescent nucleotides (SFNs) have a wide variety of applications in biochemical tracking, imaging, and diagnostic assays. There are many SFNs in active development to enhance their fluorescence wavelengths, environmental sensitivity, photostability, and photochemical/photoswitchable properties. However, there are few systematic theoretical studies of their fluorescence properties. In this work, we apply excited state QM/MM dynamics with TDDFT to nucleic acids tagged with perylene, which is particularly photostable, fluorescent and bright (fluorescence quantum yield = 0.94) in isolation. We probe the importance of geometry, dynamics, and functionalization location of the perylene tag on the nucleobase. We confirm charge transfer pathways consistent with previous experiments within our 2 ps timescale, and note that the directionality of the electron transfer stems primarily from the nucleic acid type. Additionally, we find that the functionalization point on specific nucleobases, along with key dihedral angles and orbital overlap, directly influences the probability of charge transfer and thus the final SFN fluorescence properties.