Coarse-grained modelling of the structural properties of DNA origami

Autor: Snodin, Benedict E. K., Schreck, John S., Romano, Flavio, Louis, Ard A., Doye, Jonathan P. K.

Publikováno v: Nucleic Acids Res. 47, 1585-1597 (2019)

We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origamis, focussing on archetypal 2D and 3D origamis. The model reproduces well the characteristic pattern of helix bending i

Externí odkaz: http://arxiv.org/abs/1809.08430

Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

Autor: Snodin, Benedict E. K., Randisi, Ferdinando, Mosayebi, Majid, Sulc, Petr, Schreck, John S., Romano, Flavio, Ouldridge, Thomas E., Tsukanov, Roman, Nir, Eyal, Louis, Ard A., Doye, Jonathan P. K.

Publikováno v: J. Chem. Phys. 142, 234901 (2015)

We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by slightly mo

Externí odkaz: http://arxiv.org/abs/1504.00821

Tento výsledek nelze pro nepřihlášené uživatele zobrazit.
K zobrazení výsledku je třeba se přihlásit.

The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.

Autor: Doye JPK; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK. jonathan.doye@chem.ox.ac.uk., Fowler H; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK., Prešern D; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK., Bohlin J; Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK., Rovigatti L; Dipartimento di Fisica, Sapienza Universitá di Roma, Rome, Italy., Romano F; Dipartimento di Fisica, Sapienza Universitá di Roma, Rome, Italy., Šulc P; School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA., Wong CK; Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK., Louis AA; Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford, UK., Schreck JS; Computational and Information Systems Laboratory, National Center for Atmospheric Research (NCAR), Boulder, USA., Engel MC; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA., Matthies M; School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA., Benson E; Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK., Poppleton E; School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA., Snodin BEK; Department of Philosophy, Future of Humanity Institute, University of Oxford, Oxford, UK.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2023; Vol. 2639, pp. 93-112.