Protein: Nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes

Abstract

Low singlet transition energies and line strengths were calculated for the cytosine:indole:guanine complex by the INDO/1S-CI method. The chromophores were arranged in three sets of 270 intercalating geometries. Calculations were executed in the supermolecule model with single excited configurations. Errors due to basis set extension and incomplete configuration representation were assessed, for all chromophore pairs, by full BSSE correction calculations and inclusion of double-excited configurations. The intercalation-induced perturbations of the principal transitions are characterized by but not limited to (a) a decrease in strength of [pi*,pi] transitions, (b) increase in strength in [pi*,n] transitions, (c) splitting of [pi*,pi] transitions into components of unequal strength, and (d) energy and strength dependence in mixed transitions on rise and shift movements of the nucleic acid bases. These predictions are in accord with absorption, fluorescence emission, and scattering, and resonance Raman spectroscopic data on oligonucleotides and analogous aromatic complexes. The calculations suggest that major differences in intercalating coordinations are discernible in the near-uv spectroscopic domain of proteins and nucleic acids.

Conformation of xanthene dyes in the sulfhydryl 1 binding site of myosin

“…Valeur and Weber (1977) measured the anisotropy from immobilized tryptophan and showed that under our experimental conditions all emission occurs from the 'La transition band with limiting anisotropy, r = 0.3. We used published semiempirical calculations of indole electronic dipole transition moments to orient the two higher energy transitions, 'A -'Ba and 'A -* 'Bb, within the indole ring (Goux et al, 1976;Ilich & Prendergast, 1992). We assume that they too emit through the 'La emission dipole.…”