Results 31 to 40 of about 2,257,590 (274)
Improved Bayesian methods for detecting recombination and rate heterogeneity in DNA sequence alignments [PDF]
, 2011 DNA sequence alignments are usually not homogeneous. Mosaic structures may result as a consequence of recombination or rate heterogeneity. Interspecific recombination, in which DNA subsequences are transferred between different (typically viral or ...
Mantzaris, Alexander Vassilios +1 more
core +3 more sources
Model for topology dependent DNA binding
, 2023 This package contains code that implements a model for topology-dependent binding to ...
Jan Lipfert (Utrecht University)
core +1 more source
A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2. [PDF]
PLoS Genetics, 2012 DNA topology has fundamental control over the ability of transcription factors to access their target DNA sites at gene promoters. However, the influence of DNA topology on protein-DNA and protein-protein interactions is poorly understood.
Andrew D S Cameron, Charles J Dorman
doaj +1 more source
DNA Mechanics and Topology [PDF]
, 2018 We review the current understanding of the mechanics of DNA and DNA-protein complexes, from scales of base pairs up to whole chromosomes. Mechanics of the double helix as revealed by single-molecule experiments will be described, with an emphasis on the role of polymer statistical mechanics.
Sumitabha, Brahmachari, John F, Marko
openaire +2 more sources
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
The organizer of chromatin topology RIF1 ensures cellular resilience to DNA replication stress
Life Science Alliance, 2023 The conserved protein RIF1 stabilizes replication factories and regulates cohesin recruitment in response to replication stress to limit DNA lesions. Eukaryotic genomes are duplicated from thousands of replication origins that fire sequentially forming a
Rana Lebdy +6 more
doaj +1 more source
Untangling intracellular DNA topology [PDF]
Molecular Microbiology, 2004 SummaryThe biochemical steps by which bacterial topoisomerases alter the topology of DNA are well known. However, it has been a more vexing task to establish physiological roles and sites of action of the different topoisomerases within the context of the bacterial cell cycle.
Olivier, Espeli, Kenneth J, Marians
openaire +2 more sources
Tuning the topology of a two-dimensional catenated DNA network
Physical Review Research, 2023 Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast. Restriction enzymes that
Indresh Yadav +2 more
doaj +1 more source
Topological Behavior of Plasmid DNA [PDF]
Microbiology Spectrum, 2014 ABSTRACT The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and ...
N Patrick, Higgins +1 more
openaire +2 more sources
Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases [PDF]
, 2010 ype II DNA topoisomerases are ubiquitous enzymes with essential functions in DNA replication, recombination and transcription. They change DNA topology by forming a transient covalent cleavage complex with a gate-DNA duplex that allows transport of a ...
Laponogov, I +27 more
core +1 more source