ArticleNucleic acids research2007
Base-flipping dynamics in a DNA hairpin processing reaction.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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.
The trial behind it
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
24 citing papers in PubMed.
- The telomere resolvase, TelA, utilizes an underwound pre-cleavage intermediate to promote hairpin telomere formation.PloS one · 2023Article
- Energy Landscapes for Base-Flipping in a Model DNA Duplex.The journal of physical chemistry. B · 2022Article
- Hijacking Transposable Elements for Saturation Mutagenesis in Fungi.Frontiers in fungal biology · 2021Review
- Structural basis of seamless excision and specific targeting by piggyBac transposase.Nature communications · 2020Article
- Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features.Science (New York, N.Y.) · 2019Article
- Transposase subunit architecture and its relationship to genome size and the rate of transposition in prokaryotes and eukaryotes.Nucleic acids research · 2018Article
- Article
- A single active site in the mariner transposase cleaves DNA strands of opposite polarity.Nucleic acids research · 2017Article
- Biochemical Characterization of Kat1: a Domesticated hAT-Transposase that Induces DNA Hairpin Formation and MAT-Switching.Scientific reports · 2016Article
- Chemical display of pyrimidine bases flipped out by modification-dependent restriction endonucleases of MspJI and PvuRts1I families.PloS one · 2014Article
- H-NS mediates the dissociation of a refractory protein-DNA complex during Tn10/IS10 transposition.Nucleic acids research · 2011Article
- A simple topological filter in a eukaryotic transposon as a mechanism to suppress genome instability.Molecular and cellular biology · 2011Article
- Review
- Delivering the goods: viral and non-viral gene therapy systems and the inherent limits on cargo DNA and internal sequences.Genetica · 2010Review
- Integrating prokaryotes and eukaryotes: DNA transposases in light of structure.Critical reviews in biochemistry and molecular biology · 2010Review
- Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage.Nucleic acids research · 2010Article
- Article
- Base flipping in V(D)J recombination: insights into the mechanism of hairpin formation, the 12/23 rule, and the coordination of double-strand breaks.Molecular and cellular biology · 2009Article
- Article
- The global bacterial regulator H-NS promotes transpososome formation and transposition in the Tn5 system.Nucleic acids research · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Many enzymes that repair or modify bases in double-stranded DNA gain access to their substrates by base flipping. Although crystal structures provide stunning snap shots, biochemical approaches addressing the dynamics have proven difficult, particularly in complicated multi-step reactions. Here, we use protein-DNA crosslinking and potassium permanganate reactivity to explore the base-flipping step in Tn5 transposition. We present a model to suggest that base flipping is driven by a combination of factors including DNA bending and the intrusion of a probe residue. The forces are postulated to act early in the reaction to create a state of tension, relieved by base flipping after cleavage of the first strand of DNA at the transposon end. Elimination of the probe residue retards the kinetics of nicking and reduces base flipping by 50%. Unexpectedly, the probe residue is even more important during the hairpin resolution step. Overall, base flipping is pivotal to the hairpin processing reaction because it performs two opposite but closely related functions. On one hand it disrupts the double helix, providing the necessary strand separation and steric freedom. While on the other, transposase appears to position the second DNA strand in the active site for cleavage using the flipped base as a handle.
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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.