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
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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
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
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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
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DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. [PDF]
PLoS Computational BiologyIn eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin ...
Chunhong Long, Hongqiong Liang, Biao Wan
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Differential effect of supercoiling on bacterial transcription in topological domains. [PDF]
PLoS Computational BiologyDNA supercoiling (SC), the over- and under-winding of DNA, is generated by transcription as described in the twin-domain model. Conversely, SC also impacts transcription through torsional stress.
Boaz Goldberg +3 more
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Susceptibility to superhelically driven DNA duplex destabilization: a highly conserved property of yeast replication origins. [PDF]
PLoS Computational Biology, 2005 Strand separation is obligatory for several DNA functions, including replication. However, local DNA properties such as A+T content or thermodynamic stability alone do not determine the susceptibility to this transition in vivo.
Prashanth Ak, Craig J Benham
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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
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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
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Supercoiling Effects on Short-Range DNA Looping in E. coli. [PDF]
PLoS ONE, 2016 DNA-protein loops can be essential for gene regulation. The Escherichia coli lactose (lac) operon is controlled by DNA-protein loops that have been studied for decades.
Lauren S Mogil +2 more
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