Computational Design And Characterization Of New Thieno-Expanded Tricyclic Purine Analogs

Unnatural nucleobases are under intense research due to their widespread applications in nucleic acids research. In this work, four new thieno-expanded purine analogs comprising (ttz)A, (tth)A, (ttz)G, and (tth)G were computationally designed based on the isomorphic tz- and th-bases. These base analogs can also be seen as modified derivatives of the previously reported tricyclic purine analogs ((tt)A and (tt)G). The structural, electronic, and photophysical properties are studied by means of DFT and TDDFT calculations. We find out that these new bases can form stable Watson-Crick base pairs with natural counterparts, thus potentially mimicking natural nucleobases in DNA/RNA duplexes. Calculations reveal that these bases have smaller AIPs and HOMO-LUMO gaps than natural ones, suggesting that they are candidates for applications in nanowire technology. Particularly, the photophysical properties were explored, and the results are compared with those for tz-, th-, and tt-bases. The nature of the low-lying excited states is discussed, and analyses reveal that the thiophene-homologation would not change excitation maxima of (th)A and (tz)A, while it will result in large red-shifts of those of (th)G and (tz)G. Meanwhile, thiophene insertion has relatively larger influences on the emissions (th)A and (tz)G, for which the fluorescence was 37 nm blue-shifted and 19 nm red-shifted, respectively. Taking these new bases as derivatives of (tt)A and (tt)G, it was found that the modifications would result in large red-shifts of both the excitation maxima and the fluorescence. The effects of water solution and base paring on the phtotophysical properties were also considered.