Results 71 to 80 of about 2,295,017 (227)

Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.

PLoS Computational Biology
DNA supercoiling-the level of twisting and writhing of the DNA molecule around itself-plays an important role in the regulation of gene expression in bacteria by modulating promoter activity.
Théotime Grohens, Sam Meyer, Guillaume Beslon   +2 more
doaj   +1 more source

Genome scale patterns of supercoiling in a bacterial chromosome

Nature Communications, 2016
Bacterial DNA primarily exists in a negatively supercoiled or under-wound state. Here, by mapping the supercoiling state, the authors show that there is a gradient of supercoiling across the bacterial chromosome with the terminus being more negatively ...
Avantika Lal, Amlanjyoti Dhar, Andrei Trostel, Fedor Kouzine, Aswin S. N. Seshasayee, Sankar Adhya   +5 more
doaj   +1 more source

Probing hyper-negatively supercoiled mini-circles with nucleases and DNA binding proteins. [PDF]

PLoS ONE, 2018
It is well accepted that the introduction of negative supercoils locally unwinds the DNA double helix, influencing thus the activity of proteins. Despite the use of recent methods of molecular dynamics simulations to model the DNA supercoiling-induced ...
Carole Saintomé, Emmanuelle Delagoutte
doaj   +1 more source

Interplay of DNA supercoiling and catenation during the segregation of sister duplexes [PDF]

, 2017
The discrete regulation of supercoiling, catenation and knotting by DNA topoisomerases is well documented both in vivo and in vitro, but the interplay between them is still poorly understood. Here we studied DNA catenanes of bacterial plasmids arising as
Hernández, Pablo, Krimer, Dora B., Martínez-Robles, María Luisa, Schvartzman, Jorge B., Stasiak, Andrzej, Witz, Guillaume   +5 more
core  

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations

, 2010
Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional regulation.
Alberts, Ashburner, Babu, Ball, Beloin, Berger, Bertin, Bianca Sclavi, Blot, Boccard, Bradley, Bruno Bassetti, Cabrera, Cabrera, Cases, Chilcott, Cho, Cho, Cook, Cunha, Cunha, Dame, Darling, Dillon, Dorman, Duan, Eisen, Esnault, Espéli, Espéli, Fang, Gama-Castro, Grainger, Hengen, Hengge, Janga, Jeong, Jin, Junier, Kahramanoglou, Kalir, Kalir, Kelly, Keseler, Ko, Korea, Krin, Képès, Képès, Lang, Liu, Luijsterburg, Marco Cosentino Lagomarsino, Marr, Mathelier, Mercier, Moulin, Muskhelishvili, Nielsen, Oberto, Ogasawara, Oshima, Pesavento, Peter, Postow, Prigent-Combaret, Prüss, Reyes-Lamothe, Rocha, Saldana, Serres, Smith, Sonnenschein, Soutourina, Soutourina, Soutourina, Travers, Valens, Vittore F. Scolari, Vora, Wade, Wang, Wang, Wang, Warren, Weber, Wiggins, Wright, Zechiedrich, Zimmerman   +89 more
core   +2 more sources

Simulation of DNA Supercoil Relaxation [PDF]

Biophysical Journal, 2016
Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead.
Ikenna D, Ivenso, Todd D, Lillian
openaire   +2 more sources

Multiscale Architecture and Mechanics of the Cell Nucleus: Implications for Disease, Bioengineering and Nanomedicine

Advanced Science, EarlyView.
Nuclear mechanical properties are inherently scale‐dependent, arising from a hierarchical architecture that spans DNA, chromatin, the nuclear envelope, and condensates. Experimental techniques and theoretical models are integrated into a cohesive multiscale framework linking nanoscale structural features to organelle‐level mechanical behavior.
Xinran Liu, Xin Chen, Qingyang Zhao, Weikang Tan, Lingrui Zhu, Kin Liao, Vincent Chan, Nicolae Goga, Winfred O. Larkotey, Yang Li, Yinghui Shi, Wenya Shu, Lin Wang, Weiqing Wang, Tian Jian Lu, Yulong Han   +15 more
wiley   +1 more source

Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates

Biology, 2021
DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined.
Jorge Cebrián, Victor Martínez, Pablo Hernández, Dora B. Krimer, María-José Fernández-Nestosa, Jorge B. Schvartzman   +5 more
doaj   +1 more source

Macroscopic loop formation in circular DNA denaturation

, 2012
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured ...
Alkan Kabakçıoğlu, Amir Bar, B. Alberts, David Mukamel   +3 more
core   +3 more sources

Transcription as a Threat to Genome Integrity [PDF]

, 2016
Genomes undergo different types of sporadic alterations, including DNA damage, point mutations, and genome rearrangements, that constitute the basis for evolution.
Aguilera López, Andrés, Gaillard, Hélène   +1 more
core   +1 more source