ArticleNucleic acids research2004
Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3' polypurine tract.
Article in Nucleic acids research, 2004. 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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Who cites it
40 citing papers in PubMed, 70 citations in OpenAlex.
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- Cell cycle regulated DNA methyltransferase: fluorescent tracking of a DNA strand-separation mechanism and identification of the responsible protein motif.Nucleic acids research · 2020Article
- Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase.The Journal of biological chemistry · 2018Article
- Characterization of the C-Terminal Nuclease Domain of Herpes Simplex Virus pUL15 as a Target of Nucleotidyltransferase Inhibitors.Biochemistry · 2016Article
- Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes.Frontiers in chemistry · 2016Review
- Reverse Transcription of Retroviruses and LTR Retrotransposons.Microbiology spectrum · 2015Review
- RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.Nature structural & molecular biology · 2014Article
- Functionalized tricyclic cytosine analogues provide nucleoside fluorophores with improved photophysical properties and a range of solvent sensitivities.Chemistry (Weinheim an der Bergstrasse, Germany) · 2014Article
- HIV-1 reverse transcription.Cold Spring Harbor perspectives in medicine · 2012Review
- The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.Nucleic acids research · 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
- Synthetic nucleotides as probes of DNA polymerase specificity.Journal of nucleic acids · 2012Article
- Probing Retroviral and Retrotransposon Genome Structures: The "SHAPE" of Things to Come.Molecular biology international · 2012Article
- Fluorescent DNA-based enzyme sensors.Chemical Society reviews · 2011Review
- Solid-Phase Synthesis of 5'-O-β,γ-Methylenetriphosphate Derivatives of Nucleosides and Evaluation of Their Inhibitory Activity Against HIV-1 Reverse Transcriptase.Tetrahedron letters · 2010Article
- Fluorescent analogs of biomolecular building blocks: design, properties, and applications.Chemical reviews · 2010Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Recent structural analyses indicate that localized regions of abnormal base pairing exist within RNA/DNA hybrids containing the HIV-1 polypurine tract (PPT) and that these distortions may play a role in PPT function. To examine this directly, we have introduced pyrrolo-deoxycytosine (pdC), a fluorescent, environmentally sensitive analog of deoxycytosine (dC), into the DNA strand of PPT-containing hybrids. Steady-state fluorescence analysis of these hybrids reveals that the DNA base 11 nt from the PPT-U3 junction is unpaired even in the absence of reverse transcriptase (RT). Unstable base pairing is also observed within the (rG:dC)6 tract in the downstream portion of the duplex, suggesting that HIV-1 RT may recognize multiple pre-existing distortions during PPT selection. HIV-1 RT hydrolyzes pdC-containing hybrids primarily at the PPT-U3 junction, indicating that the analog does not induce a gross structural deformation of the duplex. However, aberrant cleavage is frequently observed 3 bp from the site of pdC substitution, most likely reflecting a specific interaction between the analog and amino acid residues within the RNase H primer grip. pdC substitution within the template strand of a DNA duplex does not appear to significantly affect RT-catalyzed DNA synthesis. Implications of these findings on the use of pdC to examine nucleic acid structure are discussed.
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