ArticleFaraday discussions2019
Measuring local conformations and conformational disorder of (Cy3)
Article in Faraday discussions, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- The intrinsically disordered C-terminal domain of bacteriophage T4 gp32 amplifies pre-existing conformational heterogeneity at DNA replication junctions.bioRxiv : the preprint server for biology · 2026Article
- Site-specific free energy surface parameters from single-molecule fluorescence measurements of exciton-coupled (iCy3)2 dimer probes positioned at DNA replication fork junctions.Nucleic acids research · 2025Article
- Interferometric excitation fluorescence lifetime imaging microscopy.Nature communications · 2024Article
- Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA.The journal of physical chemistry. B · 2024Article
- Article
- Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites.Nucleic acids research · 2024Article
- Studies of DNA 'Breathing' by Polarization-Sweep Single-Molecule Fluorescence Microscopy of Exciton-Coupled (iCy3)The journal of physical chemistry. B · 2023Article
- Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer.The journal of physical chemistry. A · 2023Article
- Pursuing excitonic energy transfer with programmable DNA-based optical breadboards.Chemical Society reviews · 2023Review
- Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer.Physical chemistry chemical physics : PCCP · 2023Article
- Electronic Structure and Excited-State Dynamics of DNA-Templated Monomers and Aggregates of Asymmetric Polymethine Dyes.The journal of physical chemistry. A · 2023Article
- Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy.Annual review of physical chemistry · 2023Review
- Mechanism of strand displacement DNA synthesis by the coordinated activities of human mitochondrial DNA polymerase and SSB.Nucleic acids research · 2023Article
- Article
- Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines.The journal of physical chemistry. A · 2023Article
- Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction.The journal of physical chemistry letters · 2022Article
- Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes.The journal of physical chemistry. C, Nanomaterials and interfaces · 2022Article
- Symmetry Breaking Charge Transfer in DNA-Templated Perylene Dimer Aggregates.Molecules (Basel, Switzerland) · 2022Article
- Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays.Methods (San Diego, Calif.) · 2022Review
- Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The sugar-phosphate backbone of DNA near single-stranded (ss)-double-stranded (ds) junctions likely fluctuates within a broad distribution of conformations to permit the proper binding of genome regulatory proteins that function at these sites. In this work we use absorbance, circular dichroism (CD), and two-dimensional fluorescence spectroscopy (2DFS) to study the local conformations and conformational disorder within chromophore-labeled DNA constructs. These constructs employ dimers of the fluorescent chromophore Cy3 that are site-specifically incorporated into the sugar-phosphate backbones of DNA strands at ss-ds DNA fork junctions. We show that these data can be analyzed to determine the local conformations of the (Cy3)2 dimer, and the degree of conformational disorder. Our analysis employs an essential-state Holstein-Frenkel Hamiltonian model, which takes into account the internal electronic-vibrational motions within each Cy3 chromophore, and the resonant electronic interaction that couples the two chromophores together. Our results suggest that this approach may be applied generally to understand local backbone conformation and conformational disorder at ss-ds DNA fork junctions.
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