ArticleProceedings of the National Academy of Sciences of the United States of America2005
Investigating local conformations of double-stranded DNA by low-energy circular dichroism of pyrrolo-cytosine.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
- Impacts of sequence and structure on pyrrolocytosine fluorescence in RNA.Nucleic acids research · 2025Article
- Identifying and Differentiating Topological G-Quadruplex Structures with DNA-Encoded Plasmonic Gold Nanoparticles.Angewandte Chemie (International ed. in English) · 2022Article
- 6-phenylpyrrolocytosine as a fluorescent probe to examine nucleotide flipping catalyzed by a DNA repair protein.Biopolymers · 2021Article
- Local DNA Base Conformations and Ligand Intercalation in DNA Constructs Containing Optical Probes.Biophysical journal · 2019Article
- RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.Nature structural & molecular biology · 2014Article
- Fifty years of DNA "breathing": Reflections on old and new approaches.Biopolymers · 2013Review
- Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states.Journal of the American Chemical Society · 2012Article
- Characterization of the 6-methyl isoxanthopterin (6-MI) base analog dimer, a spectroscopic probe for monitoring guanine base conformations at specific sites in nucleic acids.Nucleic acids research · 2012Article
- Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing.Nucleic acids research · 2011Article
- Evaluation of fluorescent analogs of deoxycytidine for monitoring DNA transitions from duplex to functional structures.Journal of nucleic acids · 2011Article
- DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Fluorescent analogs of biomolecular building blocks: design, properties, and applications.Chemical reviews · 2010Review
- DNA models of trinucleotide frameshift deletions: the formation of loops and bulges at the primer-template junction.Nucleic acids research · 2009Article
- Spectroscopic studies of position-specific DNA "breathing" fluctuations at replication forks and primer-template junctions.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation.RNA (New York, N.Y.) · 2006Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Local base stacking and conformational mobility play a major role in the structure and function of nucleic acids. We have recently shown that the low-energy CD spectrum of 2-aminopurine (2-AP), i.e., the CD spectral region above 300 nm, can be used to monitor conformational changes in polynucleotides at or near mono- and dinucleotide 2-AP residues that replace adenine residues in DNA and RNA. Here, we extend this technique to pyrrolo-cytosine (PC), a fluorescent analogue of cytosine. The low-energy CD spectrum of a PC dinucleotide in dsDNA exhibits an exciton couplet with two bands of opposite sign centered at 350 nm. This signal is characteristic of base stacking between adjacent PC residues in a right helical conformation. Isolated PC nucleotide residues inserted into polynucleotide chains also display chirality that reflects the asymmetric environment of their sequence context. Thus, we show that the low-energy CD spectra of C(PC)A and A(PC)C sequences in dsDNA have opposite signs. It appears that the measurement of the low-energy CD spectra of PC residues will usefully complement 2-AP measurements by serving to characterize the local conformations and dynamics of nucleic acids near C residues and G-C base pairs.
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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.