Journal of Molecular Graphics and Modelling
Journal of Molecular Graphics and Modelling
3 years ago

A new size-expanded RNA alphabet: Computational design of benzo-homologated (xtz-) isothiazole RNA and comparisons to the x-thieno RNA

A new size-expanded RNA alphabet: Computational design of benzo-homologated (xtz-) isothiazole RNA and comparisons to the x-thieno RNA
Fluorescent nucleobase analogs are of great interest because of their widespread applications in nucleic acids research. In the present work, a new benzo-homologated RNA alphabet comprising xtzA, xtzG, xtzC, and xtzU was computationally designed based on the isomorphic tz-bases. The structural, electronic, and photophysical properties are studied by means of DFT and TDDFT calculations, and the effects of water solution, ribose, and base pairing on the singlet excited transitions were examined. The results are compared with those for tz-bases and xth-bases. These new base analogs can form stable Watson-Crick base pairs with natural counterparts as tz-bases and xth-bases do. Their ionization potentials and HOMO-LUMO gaps are in the middle of tz-bases and xth-bases: xth-base < xtz-base < tz-base. Furthermore, all xtz-bases are predicted to have smaller IPs and HOMO-LUMO gaps than natural bases and tz-bases, they are suggested to be candidates for applications in nanowire technology. The S1 states for all xtz-bases are revealed to be ππ* dominated by the configuration HOMO→LUMO. In water solution, compared with tz- or xth-bases, the lowest ππ* states are about 20.06–21.91kcal/mol red-shifted or 0.92–4.15kcal/mol blue-shifted, respectively. Linking to ribose has negligible effects on the S1 excitation energies, but it owns a larger impact on the corresponding oscillator strengths. Base pairing and water solution as a whole has very little effects on the S1 transition energies of xtzA and xtzC, but it will red-shift those for xtzG and xtzU by 6.69 and 5.30kcal/mol, respectively. All xtz-bases are expected to display visible fluorescence with the wavelengths predicted to be 540, 585, 524, and 506nm for xtzA, xtzG, xtzC and xtzU, respectively, in water solution. Though structurally very similar, the excitation maxima and fluorescence emissions of xtz- and xth-bases show distinct differences, allowing them to be distinguished from each other by their spectroscopic characters

Publisher URL: www.sciencedirect.com/science

DOI: S1093326317303698

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