Evidence for a Nonbase Stacking Effect for the Environment‐sensitive Fluorescent Base Pyrrolocytosine—Comparison with 2‐Aminopurine

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Abstract
Pyrrolocytosine (PC), is a highly fluorescent analog of the natural nucleobase cytosine. The fluorescence of PC is quenched upon helix formation but the origin of the quenching is not known. We investigated the effects of base stacking in the aqueous phase by following the fluorescence of dinucleotides and trinucleotides containing PC. The quantum yields and lifetimes (ns) (in parenthesis) obtained at 25°C were: PC‐T, 0.026 (2.0), PC‐C, 0.033 (2.5), PC‐A, 0.032 (2.7), PC‐G, 0.021 (2.0), T‐PC‐T, 0.044 (3.0) and G‐PC‐G, 0.036 (0.65 and 2.6), compared with 0.038 (2.9) for PC and 0.028 (2.1) for the nucleoside triphosphate. The results show that base stacking does not, except in the case of guanine, quench the fluorescence of PC; indeed the increased solvent shielding can enhance the emitted fluorescence. In the case of G‐PC‐G the guanines do shield the fluorescent base from the solvent but a particular environment of PC between two guanines also appears to allow a rapid nonradiative pathway, suggested to be electron transfer to the excited PC, to depopulate the excited state leading to the shorter fluorescence lifetime.