Conformational Effects on Photophysical Characteristics of C5–C5′-linked Dihydrothymine Dimers in Solution¶

Abstract

Photophysical characteristics of N-substituted C5-C5'-linked dihydrothymine dimers (1a,b[meso], meso compounds of [5R,5'S]-bi-5,6-dihydrothymines; 1a,b[rac], racemic compounds of [5R,5'R]-bi-5,6-dihydrothymines and [5S,5'S]-bi-5,6-dihydrothymines) in aqueous solution with varying contents of less-polar aprotic solvent such as tetrahydrofuran or dioxane have been investigated by UV-absorption, and steady-state and time-resolved fluorescence spectroscopies. Among the C5-C5'-linked dimers, (5R,5'S)-bi-5,6-dihydro-1-methylthymine (1a[meso]) showed a red-shifted weak UV-absorption band at 270-350 nm and excimer fluorescence emission at lambda max = 370 nm with a quantum yield (phi F) of approximately 0.1 in phosphate buffer (pH < 10) at 293 K. Racemic compound of 5,6-dihydro-1-methylthymine dimer (1a[rac]), meso and racemic compounds of 5,6-dihydro-1,3-dimethylthymine dimers (1b[meso] and 1b[rac]) in phosphate buffer were nonfluorescent under similar conditions. The UV-absorption and fluorescence spectral characteristics of 1a[meso] in aqueous solution were interpreted in terms of intramolecular stacking interactions between the dihydropyrimidine chromophores leading to a preferential "closed-shell" conformation both in the ground state and the excited singlet state. In basic solutions at pH > pKa = 11.7, the fluorescence quantum yield of 1a[meso] decreased due to a dominant "open-shell" conformation resulting from the electrostatic repulsion between the deprotonated dihydrothymine chromophores of 1a[meso] in a dianion form.

Ultrafast Excited-State Dynamics in Nucleic Acids

“…[220][221][222][223][224][225][226][227][228][229][230] The latter compounds offer intriguing possibilities for studying conformational effects on excited-state dynamics, but they have been rarely studied from a photophysical viewpoint. 227 Noncovalent interactions are responsible for other base assemblies such as aggregates of two or more π-stacked bases or hydrogen-bonded base Base multimers are complex multichromophoric systems that pose great experimental and theoretical challenges. In comparison to the monomers, there has been much less experimental work on room temperature luminescence of base multimers, particularly using time-resolved techniques.…”

“…The bases may be brought into close spatial proximity through covalent linkages, as in the di-, oligo-, and polynucleotides, which are joined by the phosphodiester linkages found in natural DNAs and RNAs. Unnatural covalent linkages are also possible. − The latter compounds offer intriguing possibilities for studying conformational effects on excited-state dynamics, but they have been rarely studied from a photophysical viewpoint . Noncovalent interactions are responsible for other base assemblies such as aggregates of two or more π-stacked bases or hydrogen-bonded base pairs.…”