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
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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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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
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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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An organometallic compound which exhibits a DNA topology-dependent one-stranded intercalation mode [PDF]
, 2016 Understanding how small molecules interact with DNA is essential since it underlies a multitude of pathological conditions and therapeutic interventions.
Adhireksan +16 more
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DNA Topology: Dynamic DNA Looping [PDF]
Current Biology, 2006 The DNA in repressive loops is often tightly bent. DNA flexibility imposes significant constraints on their topology suggesting that they may exist as perturbations in plectonemic DNA.
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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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