Topogami: Topologically Linked DNA Origami [PDF]
ACS Nanoscience Au, 2021 DNA origami is a widely used DNA nanotechnology that allows construction of two-dimensional and three-dimensional nanometric shapes. The designability and rigidity of DNA origami make it an ideal material for construction of topologically linked molecules such as catenanes, which are attractive for their potential as motors and molecular machines ...
Yusuke Sakai +4 more
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TRF2-Mediated Control of Telomere DNA Topology as a Mechanism for Chromosome-End Protection [PDF]
Molecular Cell, 2016 Delphine Benarroch-Popivker +2 more
exaly +2 more sources
The Effect of DNA Topology on Observed Rates of R-Loop Formation and DNA Strand Cleavage by CRISPR Cas12a [PDF]
Genes, 2019 Kara Van Aelst +2 more
exaly +2 more sources
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
Revised role for Hfq bacterial regulator on DNA topology. [PDF]
Sci Rep, 2018 International audienceHfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small ...
Malabirade A +9 more
europepmc +3 more sources
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
doaj +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
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
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
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