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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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
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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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Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. [PDF]
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
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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
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Reconstruction of complexes of histone and superhelical nuclear dna [PDF]
Journal of Cell Science, 1981 ABSTRACT When HeLa cells are lysed in solutions containing a non-ionic detergent and 2 M-NaCl, structures are released that retain many of the morphological features of nuclei. These nucleoids contain all the nuclear RNA and DNA but few of the proteins characteristic of chromatin. Their DNA is supercoiled and so intact.
Levin, J, Cook, P
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Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint. [PDF]
PLoS ONE, 2019 The restricted access of regulatory factors to their binding sites on DNA wrapped around the nucleosomes is generally interpreted in terms of molecular shielding exerted by nucleosomal structure and internucleosomal interactions.
Rosevalentine Bosire +9 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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Superhelical duplex destabilization and the recombination position effect. [PDF]
PLoS ONE, 2011 The susceptibility to recombination of a plasmid inserted into a chromosome varies with its genomic position. This recombination position effect is known to correlate with the average G+C content of the flanking sequences.
Cheryl L Sershen +3 more
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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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