ArticleNucleic acids research2011
Real-time detection of cruciform extrusion by single-molecule DNA nanomanipulation.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 25 citations in OpenAlex.
- How DNA secondary structures drive replication fork instability.DNA repair · 2025Review
- Advancements in Aptamer-Driven DNA Nanostructures for Precision Drug Delivery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids.International journal of molecular sciences · 2022Review
- Cruciform DNA Structures Act as Legible Templates for Accelerating Homologous Recombination in Transgenic Animals.International journal of molecular sciences · 2022Article
- Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches.Nucleic acids research · 2021Review
- Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer.International journal of molecular sciences · 2021Review
- oriD structure controls RepD initiation during rolling-circle replication.Scientific reports · 2018Article
- Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules.Nucleic acids research · 2016Article
- Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features of attC recombination sites.Nucleic acids research · 2016Article
- Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength.Nucleic acids research · 2013Article
- Mapping of single-base differences between two DNA strands in a single molecule using holliday junction nanomechanics.PloS one · 2013Article
- On the topology of chromatin fibres.Interface focus · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During cruciform extrusion, a DNA inverted repeat unwinds and forms a four-way junction in which two of the branches consist of hairpin structures obtained by self-pairing of the inverted repeats. Here, we use single-molecule DNA nanomanipulation to monitor in real-time cruciform extrusion and rewinding. This allows us to determine the size of the cruciform to nearly base pair accuracy and its kinetics with second-scale time resolution. We present data obtained with two different inverted repeats, one perfect and one imperfect, and extend single-molecule force spectroscopy to measure the torque dependence of cruciform extrusion and rewinding kinetics. Using mutational analysis and a simple two-state model, we find that in the transition state intermediate only the B-DNA located between the inverted repeats (and corresponding to the unpaired apical loop) is unwound, implying that initial stabilization of the four-way (or Holliday) junction is rate-limiting. We thus find that cruciform extrusion is kinetically regulated by features of the hairpin loop, while rewinding is kinetically regulated by features of the stem. These results provide mechanistic insight into cruciform extrusion and help understand the structural features that determine the relative stability of the cruciform and B-form states.
Indexed as
Identifiers
What OpenQuestion holds
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.