Theoretical study of the structural and optical properties of cytosine analogues

Abstract

Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we use theoretical calculations to investigate the structural and optical properties of four cytosine analogues (termed as C1, C2, C3, and C4), and also consider the effects of aqueous solution and base pairing. The results show that the fluorescent cytosine analogues can pair with guanosine (G) to form stable H-bonded WC base pairs. The excited state geometries of cytosine analogues are similar to the ground geometries. The absorption maxima of the cytosine analogues are greatly red shifted compared with nature cytosine (C). The calculated absorption peaks of modified deoxyribonucleosides are in good agreement with the experimental data. The solvent effects can induce a small blue shift for C1 and C2 but a little red shift for C3 and C4, and can increase the oscillator strengths in both the absorption and emission spectra. With regard to the WC base pairs, the B3LYP functional reveals that the lowest energy transitions of GC base pairs are charge transfer excitation while the CAM-B3LYP functional predicts that they are localized excitation. The M062X and CAM-B3LYP functional show good agreement with respect to both the value of the lowest energy transitions as well as the oscillator strengths.