DNA, RNA and protein interactions

Effect of nucleic acid binding on the triplet state properties of tetrapeptides containing tryptophan and 6-methyltryptophan: a study by phosphorescence and ODMR spectroscopy

Complexes of four peptides [KWGK, KGWK, K(6MeW)GK, KG(6MeW)K] with the nucleic acids [poly(A), poly(C), poly(U), poly(I), and rG(8)] have been investigated by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The intrinsic spectroscopic probes used in these studies are tryptophan (W) and 6-methyltryptophan (6MeW). Binding to the nucleic acids results in a red-shift of the phosphorescence 0,0-band (delta E(0,0)) of the aromatic residue as well as a reduction of its zero-field splitting parameter (delta D). Results are compared with earlier studies of the HIV-1 nucleocapsid protein, NCp7, that contains a single tryptophan residue (Trp37) within a retroviral zinc finger sequence. Binding of poly(A) or poly(U) to the tetrapeptides induces larger delta E(0,0) and delta D than when bound to NCp7, indicating stronger stacking interactions. Poly(I), on the other hand, produces larger shifts in Trp37 of NCp7. Binding of rG(8) produces sequence-dependent effects in the peptides. When bound to NCp7, but in contrast with tetrapeptide binding, nucleic acids produce large changes in triplet state kinetics consistent with enhanced spin-orbit coupling. These results are discussed in terms of three limiting types of tryptophan-base interaction: intercalation, aromatic stacking, and edge-on interaction. These should have differing effects on the properties of the triplet state.

Effect of stacking interactions with poly(riboadenylic acid) on the triplet state properties of tryptophan

Optically detected magnetic resonance (ODMR) signals of tryptophan (Trp) have been measured in L-lysyl-L-tryptophyl-L-lysine (Lys-Trp-Lys) and in its complex with poly(riboadenylic acid) [poly(rA)]. Measurements were made with optical narrow band detection through the Trp O-O band. Plots of [D] and [E] vs. lambda are distinctly different for Lys-Trp-Lys and its complex with poly(rA). A reduction of [D], in particular, is consistent with stacking of Trp with adenine in the complex, since this effect is expected from charge-transfer contributions in the excited triplet state. Triplet energy transfer from poly(rA) to Lys-Trp-Lys is nearly complete at 77 K, with a Trp:adenine ratio of 0.1. The energy transfer efficiency is considerably reduced at 4.2 K and below, probably resulting from reduction of the triplet mobility in the polymer. Analysis of the phosphorescence decays shows that the triplet states of poly(rA), Lys-Trp-Lys, and their complex decay nonexponentially. Binding of polylysine to poly(rA) has no effect on the phosphorescence spectrum, but the decay kinetics are changed.