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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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
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PCR-Free Site-Directed Mutagenesis on Repetitive Sequences Using Single-Stranded DNA-Assisted Double-Stranded DNA Nicking by DNAzymes. [PDF]
Angew Chem Int Ed EnglWe describe single‐stranded DNA‐assisted double‐stranded DNA nicking by DNAzymes (DANDA), in which DNAzymes are used to sequence‐specifically nick or cleave superhelical plasmids, with help from assisting single‐stranded DNAs. The DANDA system can be used for PCR‐free site‐directed mutagenesis on plasmids to create mutations on difficult targets such ...
Lyu M, Kong L, Shao X, Lu Y.
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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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Non-canonical DNA structures: Diversity and disease association
Frontiers in Genetics, 2022 A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA.
Aparna Bansal +4 more
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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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TALEs from a spring--superelasticity of Tal effector protein structures. [PDF]
PLoS ONE, 2014 Transcription activator-like effectors (TALEs) are DNA-related proteins that recognise and bind specific target sequences to manipulate gene expression.
Holger Flechsig
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An improved method for large-scale preparation of negatively and positively supercoiled plasmid DNA [PDF]
BioTechniques, 2009 A rigorous understanding of the biological function of superhelical tension in cellular DNA requires the development of new tools and model systems for study.
Marita C. Barth +2 more
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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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