ArticleMolecules (Basel, Switzerland)2020
Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair.
Article in Molecules (Basel, Switzerland), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 10 citations in OpenAlex.
- A Novel Label-Free Fluorescent Turn-on Method for the Determination of Guanine Using Levodopa.Journal of fluorescence · 2026Article
- Single-Molecule Chemistry Part II: Pathway Analysis of the Oxidation of Guanine to 8-Oxo-7,8-dihydroguanosine in an Oligonucleotide Hybrid.Molecules (Basel, Switzerland) · 2026Article
- Fluorescent modifications in aptamer switches-positional, structural, and neighboring pair effects on sensor performance.Nucleic acids research · 2025Article
- Fluorophore-mediated Photooxidation of the Guanine Heterocycle.Journal of physical organic chemistry · 2022Article
- Sequence-dependence of Cy3 and Cy5 dyes in 3' terminally-labeled single-stranded DNA.Scientific reports · 2022Article
- Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies.Biophysics and physicobiology · 2022Article
- Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3.The journal of physical chemistry. A · 2021Article
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2 authors at 1 institution in 1 country.
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Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7-8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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