ArticleNucleic acids research2014
Internally labeled Cy3/Cy5 DNA constructs show greatly enhanced photo-stability in single-molecule FRET experiments.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed, 76 citations in OpenAlex.
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- Fluorescent modifications in aptamer switches-positional, structural, and neighboring pair effects on sensor performance.Nucleic acids research · 2025Article
- Functional integration of the bacteriophage T4 DNA replication complex: The multiple roles of the ssDNA binding protein (gp32).bioRxiv : the preprint server for biology · 2025Article
- Indocarbocyanine-Indodicarbocyanine (sCy3-sCy5) Absorptive Interactions in Conjugates and DNA Duplexes.Molecules (Basel, Switzerland) · 2024Article
- Nuclease-induced stepwise photodropping (NISP) to precisely investigate single-stranded DNA degradation behaviors of exonucleases and endonucleases.Nucleic acids research · 2024Article
- Interferometric excitation fluorescence lifetime imaging microscopy.Nature communications · 2024Article
- Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels.Nature nanotechnology · 2024Article
- Replication of [AT/TA]Biochemistry · 2024Article
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- 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
- G3BP1 and SLU7 Jointly Promote Immune Evasion by Downregulating MHC-I via PI3K/Akt Activation in Bladder Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Optical traps induce fluorophore photobleaching by two-photon excitation.Biophysical journal · 2023Article
- Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer.The journal of physical chemistry. A · 2023Article
- Replication of [AT/TA]bioRxiv : the preprint server for biology · 2023Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
- Article
- Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy.Annual review of physical chemistry · 2023Review
- "Helicase" Activity promoted through dynamic interactions between a ssDNA translocase and a diffusing SSB protein.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
DNA constructs labeled with cyanine fluorescent dyes are important substrates for single-molecule (sm) studies of the functional activity of protein-DNA complexes. We previously studied the local DNA backbone fluctuations of replication fork and primer-template DNA constructs labeled with Cy3/Cy5 donor-acceptor Förster resonance energy transfer (FRET) chromophore pairs and showed that, contrary to dyes linked 'externally' to the bases with flexible tethers, direct 'internal' (and rigid) insertion of the chromophores into the sugar-phosphate backbones resulted in DNA constructs that could be used to study intrinsic and protein-induced DNA backbone fluctuations by both smFRET and sm Fluorescent Linear Dichroism (smFLD). Here we show that these rigidly inserted Cy3/Cy5 chromophores also exhibit two additional useful properties, showing both high photo-stability and minimal effects on the local thermodynamic stability of the DNA constructs. The increased photo-stability of the internal labels significantly reduces the proportion of false positive smFRET conversion 'background' signals, thereby simplifying interpretations of both smFRET and smFLD experiments, while the decreased effects of the internal probes on local thermodynamic stability also make fluctuations sensed by these probes more representative of the unperturbed DNA structure. We suggest that internal probe labeling may be useful in studies of many DNA-protein interaction systems.
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