ArticleBiophysical journal2011
Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Fluorescent modifications in aptamer switches-positional, structural, and neighboring pair effects on sensor performance.Nucleic acids research · 2025Article
- Time-Resolved Fluorescence Detection of Nicked DNA via Site-Specific Stacking of Sulfo-Cy3: The Role of Charge, Polarity, Linker, and Sequence Context.The journal of physical chemistry. B · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Binding Behavior of Human Hepatoma-Derived Growth Factor onThe journal of physical chemistry. B · 2024Article
- Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels.Nature nanotechnology · 2024Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
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- Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching.Nano letters · 2022Article
- Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy.The Journal of chemical physics · 2022Article
- Loquacious-PD regulates the terminus-dependent molecular recognition of Dicer-2 toward double-stranded RNA.Chemical communications (Cambridge, England) · 2021Article
- Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.RNA (New York, N.Y.) · 2021Article
- Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level.Computational and structural biotechnology journal · 2021Review
- Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair.Molecules (Basel, Switzerland) · 2020Article
- Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation.Nature communications · 2019Article
- Oligonucleotide-mediated tRNA sequestration enables one-pot sense codon reassignment in vitro.Nucleic acids research · 2018Article
- Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA.The Journal of chemical physics · 2018Article
- Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy.Nucleic acids research · 2018Article
- Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA.Biophysical journal · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We characterized the effect of the first basepair on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of double-stranded DNA using gaussian-mixture adaptive umbrella sampling simulations. In the simulations, the sampling of all five dihedral angles along the linker was enhanced, so that both stacked and unstacked states were sampled. The affinity of Cy3 for a T·A basepair (with the dye attached to T) was found to be significantly less than for the other basepairs. This was verified experimentally by measuring the activation energies for cis-trans isomerization of the dye. The simulation and experimental results indicate the existence of partially unstacked conformations amenable to photoisomerization. The simulations also showed that stacking of Cy3 straightens the DNA while stabilizing the first basepair. Our findings indicate that fluorescence is modulated by Cy3-DNA interactions in a sequence-dependent manner.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.