ИСТИНА

Specific covalent linking of the RHO–TAMRA to the DNA scaffold allows to restrict the number of possible conformations of the heterodimer1: the relative position of monomers on the DNA strand is known and the distance of the chromophore from DNA is confined by the length of the linkers. Using molecular dynamics simulations with different initial conditions, for the current design we obtain two types of the dimeric structures stable within 60ns. The lowest energy conformer (D1) have the orientation of the phenyl substituent in RHO with ortho-sulfo-group located inside the dimer subspace and TAMRA phenyl substituent with linker located outside the dimer subspace. For D1 was applied nuclear-ensemble approximation with the sampling based on localization of natural transition orbitals (NTO). Using 8ns MD trajectory run of the conformer D1 tethered on DNA with solvent and counter-ions taken into account we build our ensemble with samples taken sequentially each 20 ps (400 samples). For each sample only chromophore with linkers and nearest to the anion groups water molecules (within distance < 2.5A) were taken for TDDFT/ CAMD- B3LYP/6-311(d,p) calculations of excitation energies and oscillator strengths with the universal solvation model SMD to built the absorption profile averaged over the ensemble. The line shape was constructed by convoluting vertical electronic transitions of each snapshot with Gaussian function on the energy domain with half width at half maximum of 250 cm-1