ArticleBiophysical journal2011
Orientation of cyanine fluorophores terminally attached to DNA via long, flexible tethers.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Proximity-Based Super-Resolution Imaging Enabled by DNA Base-Stacking Interactions.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- 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
- Pursuing excitonic energy transfer with programmable DNA-based optical breadboards.Chemical Society reviews · 2023Review
- FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.eLife · 2021Review
- Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria.Microbiology and molecular biology reviews : MMBR · 2020Review
- 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
- Development of a genetically encodable FRET system using fluorescent RNA aptamers.Nature communications · 2018Article
- Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA.Biophysical journal · 2017Article
- Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy.Wiley interdisciplinary reviews. RNA · 2016Review
- Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes.Sensors (Basel, Switzerland) · 2016Review
- Bright Fluorescent Nanotags from Bottlebrush Polymers with DNA-Tipped Bristles.ACS central science · 2015Article
- The architecture of the 12RSS in V(D)J recombination signal and synaptic complexes.Nucleic acids research · 2015Article
- Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study.Biophysical journal · 2014Article
- Structure-based model for light-harvesting properties of nucleic acid nanostructures.Nucleic acids research · 2014Article
- Riboswitch structure and dynamics by smFRET microscopy.Methods in enzymology · 2014Article
- Measurement of the change in twist at a helical junction in RNA using the orientation dependence of FRET.Biophysical journal · 2013Article
- The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores.Molecular bioSystems · 2013Article
- FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids.Nucleic acids research · 2013Article
- Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation.PloS one · 2013Article
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5 authors.
Funding
Abstract
Cyanine fluorophores are commonly used in single-molecule FRET experiments with nucleic acids. We have previously shown that indocarbocyanine fluorophores attached to the 5'-termini of DNA and RNA via three-carbon atom linkers stack on the ends of the helix, orienting their transition moments. We now investigate the orientation of sulfoindocarbocyanine fluorophores tethered to the 5'-termini of DNA via 13-atom linkers. Fluorescence lifetime measurements of sulfoindocarbocyanine 3 attached to double-stranded DNA indicate that the fluorophore is extensively stacked onto the terminal basepair at 15 °C, with properties that depend on the terminal sequence. In single molecules of duplex DNA, FRET efficiency between sulfoindocarbocyanine 3 and 5 attached in this manner is modulated with helix length, indicative of fluorophore orientation and consistent with stacked fluorophores that can undergo lateral motion. We conclude that terminal stacking is an intrinsic property of the cyanine fluorophores irrespective of the length of the tether and the presence or absence of sulfonyl groups. However, compared to short-tether indocarbocyanine, the mean rotational relationship between the two fluorophores is changed by ∼60° for the long-tether sulfoindocarbocyanine fluorophores. This is consistent with the transition moments becoming approximately aligned with the long axis of the terminal basepair for the long-linker species.
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