ArticleThe Journal of chemical physics2022
Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy.
Article in The Journal of chemical physics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- 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
- Fluorescence-Detected Pump-Probe Spectroscopy for Artifact-Free Detection of Stokes Shift Dynamics.The journal of physical chemistry letters · 2025Article
- 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
- Single-molecule orientation-localization microscopy: Applications and approaches.Quarterly reviews of biophysics · 2024Review
- 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
- Sculpting photoproducts with DNA origami.Chem · 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
- Two-Dimensional Supramolecular Polymerization of DNA Amphiphiles is Driven by Sequence-Dependent DNA-Chromophore Interactions.Angewandte Chemie (International ed. in English) · 2023Article
- Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy.Annual review of physical chemistry · 2023Review
- Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines.The journal of physical chemistry. A · 2023Article
- Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures.Angewandte Chemie (International ed. in English) · 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
- Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3.Molecules (Basel, Switzerland) · 2022Article
- Two-photon excitation two-dimensional fluorescence spectroscopy (2PE-2DFS) of the fluorescent nucleobase 6-MI.Proceedings of SPIE--the International Society for Optical EngineeringArticle
- Studies of DNA breathing in exciton-coupled (iCy3)Proceedings of SPIE--the International Society for Optical EngineeringArticle
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
DNA replication and the related processes of genome expression require binding, assembly, and function of protein complexes at and near single-stranded (ss)-double-stranded (ds) DNA junctions. These central protein-DNA interactions are likely influenced by thermally induced conformational fluctuations of the DNA scaffold across an unknown distribution of functionally relevant states to provide regulatory proteins access to properly conformed DNA binding sites. Thus, characterizing the nature of conformational fluctuations and the associated structural disorder at ss-dsDNA junctions is critical for understanding the molecular mechanisms of these central biological processes. Here, we describe spectroscopic studies of model ss-dsDNA fork constructs that contain dimers of "internally labeled" cyanine (iCy3) chromophore probes that have been rigidly inserted within the sugar-phosphate backbones of the DNA strands. Our combined analyses of absorbance, circular dichroism, and two-dimensional fluorescence spectroscopy permit us to characterize the local conformational parameters and conformational distributions. We find that the DNA sugar-phosphate backbones undergo abrupt successive changes in their local conformations-initially from a right-handed and ordered DNA state to a disordered splayed-open structure and then to a disordered left-handed conformation-as the dimer probes are moved across the ss-dsDNA junction. Our results suggest that the sugar-phosphate backbones at and near ss-dsDNA junctions adopt specific position-dependent local conformations and exhibit varying extents of conformational disorder that deviate widely from the Watson-Crick structure. We suggest that some of these conformations can function as secondary-structure motifs for interaction with protein complexes that bind to and assemble at these sites.
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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.