The relaxation time for a cruciform structure in superhelical DNA
FEBS Letters, 1983 We have calculated the relaxation time of a cruciform structure in superhelical DNA as a function of the superhelix density for palindromic regions of different lengths. The relaxation time has a sharp maximum at the superhelix density which corresponds to the equilibrium transition point between the cruciform structure and the regular double helix ...
A V Vologodskii, M D Frank-Kamenetskii
exaly +4 more sources
Theoretical analysis of competing conformational transitions in superhelical DNA. [PDF]
PLoS Computational Biology, 2012 We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence.
Dina Zhabinskaya, Craig J Benham
doaj +2 more sources
Sequence and supercoiling-dependent effects on the structural dynamics of DNA minicircles [PDF]
Biophysical ReportsThe degree of over-/underwinding of the DNA double helix, quantified by the superhelical density, is a key feature modulating critical biological processes such as gene expression and regulation.
Manuel Micheloni +3 more
doaj +2 more sources
New Insights into the Geometry and Topology of DNA Replication Intermediates [PDF]
BiologyThe regulation of superhelical stress, mediated by the combined action of topoisomerases and fork rotation, is crucial for DNA replication. The conformational changes during DNA replication are still experimentally challenging, mainly due to the rapid ...
Victor Martínez +7 more
doaj +2 more sources
Nucleic Acids Res, 2023 Abstract Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs.
Benham CJ.
europepmc +3 more sources
Correction: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. [PDF]
PLoS Computational Biology, 2019 [This corrects the article DOI: 10.1371/journal.pcbi.1006024.].
Hidetoshi Kono +2 more
doaj +2 more sources
Theoretical analysis of the stress induced B-Z transition in superhelical DNA. [PDF]
PLoS Computational Biology, 2011 We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses.
Dina Zhabinskaya, Craig J Benham
doaj +2 more sources
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA.
PLoS Computational Biology, 2018 The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core.
Hidetoshi Kono +2 more
doaj +2 more sources
Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [PDF]
Nature CommunicationsTranscription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S.
William H. Gittens +4 more
doaj +2 more sources
The dissociation of nuclear proteins from superhelical DNA [PDF]
Journal of Cell Science, 1978 ABSTRACT Structures retaining many of the morphological features of nuclei may be released by gently lysing human cells in solutions containing non-ionic detergents and high concentrations of salt. These nucleoids contain superhelical DNA.
Levin, J, Jost, E, Cook, P
openaire +4 more sources