ArticleNucleic acids research2013
Competitive superhelical transitions involving cruciform extrusion.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 24 citations in OpenAlex.
- DNA superhelicity.Nucleic acids research · 2024Article
- Detection of Z-DNA Structures in Supercoiled Genome.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids.International journal of molecular sciences · 2022Review
- Insertion Sequence (IS) Element-Mediated Activating Mutations of the Cryptic Aromatic β-Glucoside Utilization (International journal of molecular sciences · 2022Article
- Non-B DNA-Forming Motifs Promote Mfd-Dependent Stationary-Phase Mutagenesis inMicroorganisms · 2021Article
- G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders.Nucleic acids research · 2020Review
- Emerging roles for R-loop structures in the management of topological stress.The Journal of biological chemistry · 2020Review
- The Rich World of p53 DNA Binding Targets: The Role of DNA Structure.International journal of molecular sciences · 2019Review
- A strong structural correlation between short inverted repeat sequences and the polyadenylation signal in yeast and nucleosome exclusion by these inverted repeats.Current genetics · 2019Article
- Interplay between DNA sequence and negative superhelicity drives R-loop structures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Requirement or exclusion of inverted repeat sequences with cruciform-forming potential in Escherichia coli revealed by genome-wide analyses.Current genetics · 2018Article
- Short inverted repeats contribute to localized mutability in human somatic cells.Nucleic acids research · 2017Article
- Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome.Cell systems · 2017Article
- Controlling gene expression by DNA mechanics: emerging insights and challenges.Biophysical reviews · 2016Review
- Controlling gene expression by DNA mechanics: emerging insights and challenges.Biophysical reviews · 2016Review
- Complexity of a small non-protein coding sequence in chromosomal region 22q11.2: presence of specialized DNA secondary structures and RNA exon/intron motifs.BMC genomics · 2015Article
- Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions.Scientific reports · 2015Article
- Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation.Nucleic acids research · 2014Article
- Genome-wide screen reveals replication pathway for quasi-palindrome fragility dependent on homologous recombination.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A DNA molecule under negative superhelical stress becomes susceptible to transitions to alternate structures. The accessible alternate conformations depend on base sequence and compete for occupancy. We have developed a method to calculate equilibrium distributions among the states available to such systems, as well as their average thermodynamic properties. Here we extend this approach to include superhelical cruciform extrusion at both perfect and imperfect inverted repeat (IR) sequences. We find that short IRs do not extrude cruciforms, even in the absence of competition. But as the length of an IR increases, its extrusion can come to dominate both strand separation and B-Z transitions. Although many IRs are present in human genomic DNA, we find that extrusion-susceptible ones occur infrequently. Moreover, their avoidance of transcription start sites in eukaryotes suggests that cruciform formation is rarely involved in mechanisms of gene regulation. We examine a set of clinically important chromosomal translocation breakpoints that occur at long IRs, whose rearrangement has been proposed to be driven by cruciform extrusion. Our results show that the susceptibilities of these IRs to cruciform formation correspond closely with their observed translocation frequencies.
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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.