ArticleRNA (New York, N.Y.)2006
Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation.
Article in RNA (New York, N.Y.), 2006. 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, 77 citations in OpenAlex.
- Isothiazologuanosine (Angewandte Chemie (International ed. in English) · 2026Article
- Impacts of sequence and structure on pyrrolocytosine fluorescence in RNA.Nucleic acids research · 2025Article
- Structure-based design of a sequence-specific RNA probe that mimics the kink-turn motif.NAR molecular medicine · 2025Article
- Probing RNA Structures and Interactions Using Fluorescence Lifetime Analyses.Methods in molecular biology (Clifton, N.J.) · 2023Article
- 8-Furylimidazolo-2'-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence.Acta crystallographica. Section C, Structural chemistry · 2022Article
- Fluorescence-based investigations of RNA-small molecule interactions.Methods (San Diego, Calif.) · 2019Article
- Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5'-UTR.Molecular bioSystems · 2017Article
- Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue.Physical chemistry chemical physics : PCCP · 2016Article
- Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes.The Journal of organic chemistry · 2016Article
- Sequence-Dependent Conformational Heterogeneity and Proton-Transfer Reactivity of the Fluorescent Guanine Analogue 6-Methyl Isoxanthopterin (6-MI) in DNA.The journal of physical chemistry. B · 2015Article
- In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage.Chembiochem : a European journal of chemical biology · 2015Article
- RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.Nature structural & molecular biology · 2014Article
- Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout.Molecular cell · 2014Article
- Single-Molecule Fluorescence Using Nucleotide Analogs: A Proof-of-Principle.The journal of physical chemistry letters · 2014Article
- The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.Nucleic acids research · 2012Article
- Thermodynamics of the multi-stage DNA lesion recognition and repair by formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence--stopped-flow pre-steady-state kinetics.Nucleic acids research · 2012Article
- Design, synthesis, and spectroscopic properties of extended and fused pyrrolo-dC and pyrrolo-C analogs.Organic letters · 2012Article
- Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine.Journal of molecular biology · 2012Article
- Folding of the hammerhead ribozyme: pyrrolo-cytosine fluorescence separates core folding from global folding and reveals a pH-dependent conformational change.RNA (New York, N.Y.) · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Pyrrolo-C (PC), or 3-[beta-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G. Due to its red-shifted absorbance, it can be selectively excited in the presence of natural nucleosides, making it a potential site-specific probe for RNA structure and dynamics. Similar to 2-aminopurine nucleoside, which base-pairs with uridine (or thymidine), PC's fluorescence becomes reversibly quenched upon base-pairing, most likely due to stacking interactions with neighboring bases. To test its utility as an RNA probe, we examined PC's fluorescent properties over a wide range of ionic strengths, pH, organic cosolvents, and temperatures. Incorporation of PC into a single-stranded RNA results in an approximately 60% reduction of fluorescence intensity, while duplex formation reduces the fluorescence by approximately 75% relative to the free ribonucleoside. We find that the fluorescence intensity of PC is only moderately affected by ionic strength, pH, and temperature, while it is slightly enhanced by organic cosolvents, making it a versatile probe for a broad range of buffer conditions. We demonstrate two applications for PC: fluorescent measurements of the kinetics of formation and dissociation of an RNA/DNA complex, and fluorescent monitoring of the thermal denaturation of the central segment of an RNA duplex. Taken together, our data showcase the potential of pyrrolo-C as an effective fluorescent probe to study RNA structure, dynamics, and function, complementary to the popular 2-aminopurine ribonucleoside.
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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.