ArticleBiochemistry2011
Structure of the 2-aminopurine-cytosine base pair formed in the polymerase active site of the RB69 Y567A-DNA polymerase.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Transcriptional Perturbations of 2,6-Diaminopurine and 2-Aminopurine.ACS chemical biology · 2022Article
- carba-Nucleopeptides (cNPs): A Biopharmaceutical Modality Formed through Aqueous Rhodamine B Photoredox Catalysis.Angewandte Chemie (International ed. in English) · 2022Article
- Determination of two-photon absorption in nucleobase analogues: a QR-DFT perspective.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2022Article
- Determinants of adenine-mutagenesis in diversity-generating retroelements.Nucleic acids research · 2021Article
- Excited State Dynamics of 8-Vinyldeoxyguanosine In Aqueous Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations.Molecules (Basel, Switzerland) · 2020Article
- Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels.Frontiers in chemistry · 2020Review
- Human mitochondrial transcription factors TFAM and TFB2M work synergistically in promoter melting during transcription initiation.Nucleic acids research · 2017Article
- RB69 DNA polymerase structure, kinetics, and fidelity.Biochemistry · 2014Review
- Engineering processive DNA polymerases with maximum benefit at minimum cost.Frontiers in microbiology · 2014Article
- Alteration in the cavity size adjacent to the active site of RB69 DNA polymerase changes its conformational dynamics.Nucleic acids research · 2013Article
- Quadruplex formation as a molecular switch to turn on intrinsically fluorescent nucleotide analogs.Nucleic acids research · 2013Article
- Using a fluorescent cytosine analogue tC(o) to probe the effect of the Y567 to Ala substitution on the preinsertion steps of dNMP incorporation by RB69 DNA polymerase.Biochemistry · 2012Article
- Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA.Biochemistry · 2012Article
- Synthetic nucleotides as probes of DNA polymerase specificity.Journal of nucleic acids · 2012Article
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Authors and funding
8 authors.
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Abstract
The adenine base analogue 2-aminopurine (2AP) is a potent base substitution mutagen in prokaryotes because of its enhanceed ability to form a mutagenic base pair with an incoming dCTP. Despite more than 50 years of research, the structure of the 2AP-C base pair remains unclear. We report the structure of the 2AP-dCTP base pair formed within the polymerase active site of the RB69 Y567A-DNA polymerase. A modified wobble 2AP-C base pair was detected with one H-bond between N1 of 2AP and a proton from the C4 amino group of cytosine and an apparent bifurcated H-bond between a proton on the 2-amino group of 2-aminopurine and the ring N3 and O2 atoms of cytosine. Interestingly, a primer-terminal region rich in AT base pairs, compared to GC base pairs, facilitated dCTP binding opposite template 2AP. We propose that the increased flexibility of the nucleotide binding pocket formed in the Y567A-DNA polymerase and increased "breathing" at the primer-terminal junction of A+T-rich DNA facilitate dCTP binding opposite template 2AP. Thus, interactions between DNA polymerase residues with a dynamic primer-terminal junction play a role in determining base selectivity within the polymerase active site of RB69 DNA polymerase.
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