New size-expanded RNA nucleobase analogs: A detailed theoretical study

Abstract

Fluorescent nucleobase analogs have attracted much attention in recent years due to their potential applications in nucleic acids research. In this work, four new size-expanded RNA base analogs were computationally designed and their structural, electronic, and optical properties are investigated by means of DFT calculations. The results indicate that these analogs can form stable Watson–Crick base pairs with natural counterparts and they have smaller ionization potentials and HOMO–LUMO gaps than natural ones. Particularly, the electronic absorption spectra and fluorescent emission spectra are calculated. The calculated excitation maxima are greatly red-shifted compared with their parental and natural bases, allowing them to be selectively excited. In gas phase, the fluorescence from them would be expected to occur around 526, 489, 510, and 462nm, respectively. The influences of water solution and base pairing on the relevant absorption spectra of these base analogs are also examined.