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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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
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
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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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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
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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
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Hittite Journal of Science and Engineering, 2019 I n this study novel triplex forming DNA probes have been designed in order to detect Ag+ ion in low concentrations. The use of triplex forming oligonucleotides is a convenient in applications of sensing biomolecules due to their sequence specificity and
Osman Doluca
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“An End to a Means”: How DNA-End Structure Shapes the Double-Strand Break Repair Process
Frontiers in Molecular Biosciences, 2020 Endogenously-arising DNA double-strand breaks (DSBs) rarely harbor canonical 5′-phosphate, 3′-hydroxyl moieties at the ends, which are, regardless of the pathway used, ultimately required for their repair.
Almudena Serrano-Benítez +4 more
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Hsmar1 transposition is sensitive to the topology of the transposon donor and the target. [PDF]
PLoS ONE, 2013 Hsmar1 is a member of the Tc1-mariner superfamily of DNA transposons. These elements mobilize within the genome of their host by a cut-and-paste mechanism.
Corentin Claeys Bouuaert +1 more
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Nature Communications, 2023 Genome topology is tied to R-loop formation and genome stability. However, the regulatory mechanism remains to be elucidated. By establishing a system to sense the connections between R-loops and genome topology states, we show that inhibiting DNA ...
Qin Li +7 more
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