Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance

Autor: Fosado, Y. A. G., Michieletto, D., Brackley, C. A., Marenduzzo, D.

We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a transcribing RN

Externí odkaz: http://arxiv.org/abs/1906.03287

A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA

Autor: Fosado, Y. A. G., Michieletto, D., Allan, J., Brackley, C., Henrich, O., Marenduzzo, D.

The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide

Externí odkaz: http://arxiv.org/abs/1608.03722

Topoisomerase-modulated genome-wide DNA supercoiling domains colocalize with nuclear compartments and regulate human gene expression.

Autor: Yao Q; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., Zhu L; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., Shi Z; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., Banerjee S; Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., Chen C; Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. chongyi.chen@nih.gov.

Publikováno v: Nature structural & molecular biology [Nat Struct Mol Biol] 2024 Aug 16. Date of Electronic Publication: 2024 Aug 16.

Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

Autor: Davide Michieletto, Chris A. Brackley, Yair Augusto Gutierrez Fosado, Davide Marenduzzo

Publikováno v: Proc Natl Acad Sci U S A
Fosado, Y A G, Michieletto, D, Brackley, C A & Marenduzzo, D 2021, ' Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling ', Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 10, e1905215118, pp. 1-6 . https://doi.org/10.1073/pnas.1905215118

We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide–resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d8a2b2e39971ac6621e5d081e79a2543
https://doi.org/10.1073/pnas.1905215118

Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement.

Autor: Haley NEC; Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK., Ouldridge TE; Imperial College Centre for Synthetic Biology and Department of Bioengineering, Prince Consort Road, Imperial College London, London, SW7 2AZ, UK. t.ouldridge@imperial.ac.uk., Mullor Ruiz I; Imperial College Centre for Synthetic Biology and Department of Bioengineering, Prince Consort Road, Imperial College London, London, SW7 2AZ, UK., Geraldini A; Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Keble Road, Oxford, OX1 3NP, UK., Louis AA; Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Keble Road, Oxford, OX1 3NP, UK., Bath J; Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK., Turberfield AJ; Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK. andrew.turberfield@physics.ox.ac.uk.

Publikováno v: Nature communications [Nat Commun] 2020 May 22; Vol. 11 (1), pp. 2562. Date of Electronic Publication: 2020 May 22.