Related Experiment Video
Updated: Jul 4, 2026

The Lambda Select cII Mutation Detection System
Published on: April 26, 2018
Evidence for a nonbase stacking effect for the environment-sensitive fluorescent base pyrrolocytosine--comparison
Samantha J O Hardman1, Stanley W Botchway, Katherine C Thompson
1School of Biological and Chemical Sciences, Birkbeck University of London, London, UK.
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 degrees 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.
Related Concept Videos
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Pharmacogenetics of Phase II Enzymes: N-acetyltransferase, Thiopurine S-methyltransferase, UDP-glucuronosyltransferase
Pharmacogenetics of Drug Targets: β₂-Adrenergic Receptors, Apo E, Thymidylate Synthase
Biosynthesis of Nucleic Acids
Basicity of Heterocyclic Aromatic Amines

