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
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Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing
Cell Reports, 2021 Summary: Accumulation of topological stress in the form of DNA supercoiling is inherent to the advance of RNA polymerase II (Pol II) and needs to be resolved by DNA topoisomerases to sustain productive transcriptional elongation.
Andrés Herrero-Ruiz +6 more
doaj +1 more source
A topological analysis of difference topology experiments of condensin with topoisomerase II
Biology Open, 2020 An experimental technique called difference topology combined with the mathematics of tangle analysis has been used to unveil the structure of DNA bound by the Mu transpososome. However, difference topology experiments can be difficult and time consuming.
Soojeong Kim, Isabel K. Darcy
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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
Model for topology dependent DNA binding
, 2023 This package contains code that implements a model for topology-dependent binding to ...
Jan Lipfert (Utrecht University)
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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
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Beyond Node Degree: Evaluating AS Topology Models [PDF]
, 2012 This is the accepted version of 'Beyond Node Degree: Evaluating AS Topology Models', archived originally at arXiv:0807.2023v1 [cs.NI] 13 July 2008.Many models have been proposed to generate Internet Autonomous System (AS) topologies, most of which make ...
Mortier, R +7 more
core +4 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
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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
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