Highly effective quenching of the ultrafast radiationless decay of photoexcited pyrimidine bases by covalent modification: photophysics of 5,6-trimethylenecytosine and 5,6-trimethyleneuracil

Abstract

5,6-Trimethylenecytosine (TMC) and 5,6-trimethyleneuracil (TMU), in which the twist of the C5-C6 bond (or the pyrimidalization of C5) is strongly hindered, do not exhibit the subpicosecond excited-state lifetime characteristic of the naturally occurring pyrimidine bases. This result demonstrates the important role the out-of-plane deformation of the six-membered ring plays in the ultrafast (subpicosecond) internal conversion of photoexcited nucleobases. The dramatically shorter fluorescence lifetime of TMU ( approximately 30 ps) relative to TMC ( approximately 1.2 ns), in aqueous solution at room temperature, is attributed to the presence in TMU of an efficient, secondary nonradiative decay channel of S(1)(pipi*) involving a low-lying (1)npi* state.

Femtosecond fluorescence studies of DNA/RNA constituents

“…Based on this study, it was shown that the excited state deactivation mechanism of uracil involves an important displacement of the 5-substituent. In parallel, a picosecond fluorescence study of a "blocked" uracil, 5,6-trimethyleneuracil, showed that such geometrical constraints has a dramatic effect, leading to a substantially longer fluorescence lifetime [31,32]. The authors proposed that the reaction path involves motion of both the 5-and the 6-substituent.…”

“…A deeper understanding of these processes can only be obtained through high-level theoretical calculations. Consequently, many theoretical studies based on quantum chemistry calculations have been dedicated to uracil/thymine [18,31,[44][45][46][47][48][49][50][51][52][53][54][55], cytosine [32,47,[56][57][58][59][60][61][62][63][64][65][66][67], adenine [46,51,[68][69][70][71][72][73][74][75][76][77][78] and guanine [24,[79][80][81][82][83][84][85]…”

“…In figure 5 this reaction is schematically shown for 6-aminouracil. However, alternative quantum chemistry calculations indicate that not only the 5-substituent but also the 6-substituent are moving out of the molecular plane forming a biradical state [31,32].…”

Theoretical understanding of two-photon-induced fluorescence of isomorphic nucleoside analogs

“…[6][7][8] Modified nucleic acid residues possessing fluorescence activity in the UV-visible region improve biological and biomedical applications. 13 It is also very important to consider minimal structural and functional perturbations to design a fluorescence active nucleoside analog. 13 It is also very important to consider minimal structural and functional perturbations to design a fluorescence active nucleoside analog.…”

UV-Excitation from an Experimental Perspective: Frequency Resolved

“…Heat can subsequently be safely dissipated to the environment. When internal conversion is fast enough to prevent other photochemical reactions from taking place, the molecule will have a very short excited state lifetime, τ*, and be stable against UV photodamage [9][10][11][12] . Rapid internal conversion, when available to a molecule, diffuses electronic energy by converting it to internal energy in the ground state and therefore minimizes access to other photochemical pathways.…”