ArticleBiochemistry2009
Probing anomalous structural features in polypurine tract-containing RNA-DNA hybrids with neomycin B.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR.Nucleic acids research · 2017Article
- Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder.Current topics in microbiology and immunology · 2015Review
- Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry.Nature structural & molecular biology · 2014Article
- Article
- The essential role of stacking adenines in a two-base-pair RNA kissing complex.Journal of the American Chemical Society · 2013Article
- Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions.International journal of mass spectrometry · 2012Article
- Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract.PloS one · 2012Article
- Reverse transcriptase in motion: conformational dynamics of enzyme-substrate interactions.Biochimica et biophysica acta · 2010Review
- Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
During (-)-strand DNA synthesis in retroviruses and Saccharomyces cerevisiae LTR retrotransposons, a purine rich region of the RNA template, known as the polypurine tract (PPT), is resistant to RNase H-mediated hydrolysis and subsequently serves as a primer for (+)-strand, DNA-dependent DNA synthesis. Although HIV-1 and Ty3 PPT sequences share no sequence similarity beyond the fact that both include runs of purine ribonucleotides, it has been suggested that these PPTs are processed by their cognate reverse transcriptases (RTs) through a common molecular mechanism. Here, we have used the aminoglycoside neomycin B (NB) to examine which structural features of the Ty3 PPT contribute to specific recognition and processing by its cognate RT. Using high-resolution NMR, direct infusion FTICR mass spectrometry, and isothermal titration calorimetry, we show that NB binds preferentially and selectively adjacent to the Ty3 3' PPT-U3 cleavage junction and in an upstream 5' region where the thumb subdomain of Ty3 RT putatively grips the substrate. Regions highlighted by NB on the Ty3 PPT are similar to those previously identified on the HIV-1 PPT sequence that are implicated as contact points for substrate binding by its RT. Our findings thus support the notion that common structural features of lentiviral and LTR-retrotransposon PPTs facilitate the interaction with their cognate RT.
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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.