ArticleBiophysical journal2019
Protein Environment and DNA Orientation Affect Protein-Induced Cy3 Fluorescence Enhancement.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 38 citations in OpenAlex.
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- Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair.Methods (San Diego, Calif.) · 2024Article
- Fluorescent human RPA to track assembly dynamics on DNA.Methods (San Diego, Calif.) · 2024Article
- E. coli RecB Nuclease Domain Regulates RecBCD Helicase Activity but not Single Stranded DNA Translocase Activity.Journal of molecular biology · 2024Article
- Fluorescent human RPA to track assembly dynamics on DNA.bioRxiv : the preprint server for biology · 2023Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
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- "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
- Monitoring protein conformational changes using fluorescent nanoantennas.Nature methods · 2022Article
- Loquacious-PD regulates the terminus-dependent molecular recognition of Dicer-2 toward double-stranded RNA.Chemical communications (Cambridge, England) · 2021Article
- Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3.The journal of physical chemistry. A · 2021Article
- Probing DNA-protein interactions using single-molecule diffusivity contrast.Biophysical reports · 2021Article
- Utilizing Time-Resolved Protein-Induced Fluorescence Enhancement to Identify Stable Local Conformations One α-Synuclein Monomer at a Time.Journal of visualized experiments : JoVE · 2021Article
- Probing E. coli SSB protein-DNA topology by reversing DNA backbone polarity.Biophysical journal · 2021Article
- Transient kinetic studies of the antiviraleLife · 2021Article
- Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation byBiochemistry · 2020Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The cyanine dye Cy3 is a popular fluorophore used to probe the binding of proteins to nucleic acids as well as their conformational transitions. Nucleic acids labeled only with Cy3 can often be used to monitor interactions with unlabeled proteins because of an enhancement of Cy3 fluorescence intensity that results when the protein contacts Cy3, a property sometimes referred to as protein-induced fluorescence enhancement (PIFE). Although Cy3 fluorescence is enhanced upon contacting most proteins, we show here in studies of human replication protein A and Escherichia coli single-stranded DNA binding protein that the magnitude of the Cy3 enhancement is dependent on both the protein as well as the orientation of the protein with respect to the Cy3 label on the DNA. This difference in PIFE is due entirely to differences in the final protein-DNA complex. We also show that the origin of PIFE is the longer fluorescence lifetime induced by the local protein environment. These results indicate that PIFE is not a through space distance-dependent phenomenon but requires a direct interaction of Cy3 with the protein, and the magnitude of the effect is influenced by the region of the protein contacting Cy3. Hence, use of the Cy3 PIFE effect for quantitative studies may require careful calibration.
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Registered trials
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.