Results 1 to 10 of about 7,436 (214)

The relaxation time for a cruciform structure in superhelical DNA [PDF]

FEBS Letters, 1983
We have calculated the relaxation time of a cruciform structure in superhelical DNA as a function of the superhelix density for palindromic regions of different lengths. The relaxation time has a sharp maximum at the superhelix density which corresponds to the equilibrium transition point between the cruciform structure and the regular double helix ...
A V Vologodskii, M D Frank-Kamenetskii
exaly   +4 more sources

Sequence and supercoiling-dependent effects on the structural dynamics of DNA minicircles [PDF]

Biophysical Reports
The 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, Luca Tubiana, Raffaello Potestio, Lorenzo Petrolli   +3 more
doaj   +2 more sources

DNA superhelicity. [PDF]

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]

Biology
The 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, Edith Ruiz-Díaz, Delia Cardozo, Cristian Cappo, Christian E. Schaerer, Jorge Cebrián, Dora B. Krimer, María José Fernández-Nestosa   +7 more
doaj   +2 more sources

Structures of pentatricopeptide repeat proteins. [PDF]

Acta Crystallogr F Struct Biol Commun
A number of crystal, cryo‐EM and solution structures of pentatricopeptide repeat proteins have been solved, revealing details of how they interact with single‐stranded RNA and other proteins, as well as their conformational repertoire.Pentatricopeptide repeat (PPR) proteins constitute the largest family of RNA‐binding proteins in land plants, playing ...
Pullakhandam A, Cooper C, Small ID, Bond CS.   +3 more
europepmc   +2 more sources

Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [PDF]

Nature Communications
Transcription 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, Rachal M. Allison, Ellie M. Wright, George G. B. Brown, Matthew J. Neale   +4 more
doaj   +2 more sources

Structural basis of nucleosome remodeling by Cockayne syndrome B homologue Komagataella phaffii Rad26 [PDF]

Nature Communications
Rad26, a yeast homologue of mammalian Cockayne syndrome protein B (CSB), plays an essential role in transcription-coupled nucleotide excision repair (TC-NER).
Yutaro Fukushima, Chiaki Kinoshita, Lumi Negishi, Tomoya Kujirai, Yuki Kobayashi, Mitsuo Ogasawara, Haruhiko Ehara, Shun-ichi Sekine, Wataru Kagawa, Hitoshi Kurumizaka, Yoshimasa Takizawa   +10 more
doaj   +2 more sources

DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. [PDF]

PLoS Computational Biology
In 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
doaj   +2 more sources

Cryo-EM structure of ALC1 in an open conformation bound to a PARylated nucleosome. [PDF]

Acta Crystallogr D Struct Biol
Reanalysis 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, Bacic L, Deindl S, Gaullier G.   +3 more
europepmc   +2 more sources

Differential effect of supercoiling on bacterial transcription in topological domains. [PDF]

PLoS Computational Biology
DNA 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, Nicolás Yehya, Jie Xiao, Sam Meyer   +3 more
doaj   +2 more sources