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.
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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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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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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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Bubble statistics and positioning in superhelically stressed DNA [PDF]
Physical Review E, 2011 We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our results are obtained
B. Alberts +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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Cryo-EM Analysis of a Unique Subnucleosome Containing Centromere-Specific Histone Variant CENP-A. [PDF]
Genes CellsCryo‐EM structure of the CENP‐A–H4 octasome, which lacks H2A‐H2B, was determined at 3.66 Å. The CENP‐A–H4 octasome contains twice the amount of CENP‐A compared to the canonical CENP‐A nucleosome. It may play a role in kinetochore assembly by recruiting centromere‐specific proteins during mitosis.
Kawasaki O +4 more
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