The interaction between protonated dopamine and neutral RNA and DNA nucleosides was studied by means of density functional theory calculations in vacuum and in implicit water. On the most stable complexes formed with each of the nucleosides, the vertical absorption excitation energies were evaluated and compared with the values of separated dopamine and corresponding nucleoside. The most stable complex was formed with guanosine and the spectral changes in this complex resulted in a significant reduction of the oscillator strength of the first dopamine's transition. In the first guanosine's transition, a redshift of 0.2 eV was found combined with a reduction of the oscillator strength.

Spinach aptamer was developed as an RNA analog of the green fluorescent protein. The aptamer interacts with its ligand and modifies its electronic spectrum so that it fluoresces brightly at the wavelength of 501 nm. Song et al. investigated modifications of the ligand in their experimental study and found a molecule emitting at 523 nm upon creating a complex with the Spinach aptamer. The crystal structure of the aptamer in complex with its original ligand has been published, which enabled us to study the system computationally. In this article, we suggest several new modifications of the ligand that shift the emission maximum of the complex to even longer wavelengths. Our results are based on combined quantum mechanical/molecular mechanical calculations with DFT method used for geometry optimization and TD-DFT for calculations of absorption and emission energies.