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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Reconstruction of complexes of histone and superhelical nuclear dna
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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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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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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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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Cryo-EM structure of ALC1 in an open conformation bound to a PARylated nucleosome. [PDF]
Acta Crystallogr D Struct BiolReanalysis of a publicly available cryo‐EM dataset identifies a new conformation of the oncogenic chromatin remodeler ALC1/CHD1L bound to a PARylated nucleosome. This new structure reveals the position of the macro domain in the complex, and may help to understand the large conformational change leading to the activation of ALC1.Nucleosomes are the ...
Bridges HR +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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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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Fluctuations in superhelical DNA
Nucleic Acids Research, 1979 The effect of superhelicity on the base-pair opening probability and on the probability of occurrence of cruciform states in palindromic regions is theoretically treated. The calculations show that below the superhelix density value of -sigma=0.05 superhelicity does not appreciably affect the characteristics of DNA secondary structure fluctuations.
A V, Vologodskii +3 more
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