Coarse-grained modelling of DNA-RNA hybrids

Coarse-grained modelling of DNA-RNA hybrids

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models—oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension character...

Descrizione completa

Dettagli Bibliografici
Autori principali:	Ratajczyk, EJ, Šulc, P, Turberfield, AJ, Doye, JPK, Louis, AA
Natura:	Internet publication
Lingua:	English
Pubblicazione:	2023

Documenti analoghi

Coarse-grained modeling of DNA and DNA nanotechnology
di: Ouldridge, T, et al.
Pubblicazione: (2012)

Coarse-grained modelling of supercoiled RNA
di: Matek, C, et al.
Pubblicazione: (2015)

A nucleotide-level coarse-grained model of RNA
di: Šulc, P, et al.
Pubblicazione: (2014)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
di: Šulc, P, et al.
Pubblicazione: (2014)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
di: Sulc, P, et al.
Pubblicazione: (2012)

Sequence-dependent thermodynamics of a coarse-grained DNA model.
di: Šulc, P, et al.
Pubblicazione: (2012)

Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling
di: Doye, JPK, et al.
Pubblicazione: (2022)

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
di: Ouldridge, T, et al.
Pubblicazione: (2013)

Coarse-graining DNA for simulations of DNA nanotechnology.
di: Doye, J, et al.
Pubblicazione: (2013)

Coarse-Grained Modelling of Extreme DNA Bending
di: Harrison, R, et al.
Pubblicazione: (2014)

DNA nanotweezers studied with a coarse-grained model of DNA.
di: Ouldridge, T, et al.
Pubblicazione: (2010)

DNA nanotweezers studied with a coarse-grained model of DNA
di: Ouldridge, T, et al.
Pubblicazione: (2010)

Modelling toehold-mediated RNA strand displacement
di: Šulc, P, et al.
Pubblicazione: (2015)

Coarse-grained simulations of DNA overstretching.
di: Romano, F, et al.
Pubblicazione: (2013)

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
di: Ouldridge, T, et al.
Pubblicazione: (2011)

Coarse-grained modelling of the structural properties of DNA origami
di: Snodin, B, et al.
Pubblicazione: (2019)

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
di: Snodin, B, et al.
Pubblicazione: (2015)

Coarse-grained modelling of nucleic acids
di: Sulc, P
Pubblicazione: (2014)

Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
di: Sharma, R, et al.
Pubblicazione: (2017)

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
di: Schreck, J, et al.
Pubblicazione: (2016)

Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model
di: Harrison, R, et al.
Pubblicazione: (2019)

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
di: Fonseca, P, et al.
Pubblicazione: (2018)

Measuring internal forces in single-stranded DNA: application to a DNA force clamp
di: Engel, MC, et al.
Pubblicazione: (2020)

The interplay of supercoiling and thymine dimers in DNA
di: Lim, W, et al.
Pubblicazione: (2022)

Force-induced rupture of a DNA duplex: from fundamentals to force sensors
di: Mosayebi, M, et al.
Pubblicazione: (2015)

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami
di: Suma, A, et al.
Pubblicazione: (2019)

Bottom-up coarse-grained modeling of DNA
di: Sun, Tiedong, et al.
Pubblicazione: (2021)

DNA hybridization kinetics: zippering, internal displacement and sequence dependence.
di: Ouldridge, T, et al.
Pubblicazione: (2013)

Coarse-grained modelling of DNA and DNA self-assembly
di: Ouldridge, T
Pubblicazione: (2011)

The free-energy landscape of a mechanically bistable DNA origami
di: Wong, CK, et al.
Pubblicazione: (2022)

Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
di: Bohlin, J, et al.
Pubblicazione: (2023)

Direct simulation of the self-assembly of a small DNA origami
di: Snodin, BEK, et al.
Pubblicazione: (2016)

Coarse-grained (hybrid) integrative modeling of biomolecular interactions
di: Jorge Roel-Touris, et al.
Pubblicazione: (2020-01-01)

Coarse-grained modelling of a DNA origami force sensor
di: Sen, N
Pubblicazione: (2021)

Simulating large DNA nanostructures with a coarse-grained model
di: Snodin, B
Pubblicazione: (2016)

DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
di: Schreck, J, et al.
Pubblicazione: (2014)

Hybrid Atomistic and Coarse-Grained Model for Surfactants in Apolar Solvents
di: Sampsa Vierros, et al.
Pubblicazione: (2019-09-01)

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
di: Rodrigo V. Honorato, et al.
Pubblicazione: (2019-10-01)

Influence of ionic conditions on knotting in a coarse-grained model for DNA
di: Sarah Wettermann, et al.
Pubblicazione: (2023-01-01)

Coarse-graining polymers as soft colloids
di: Louis, A, et al.
Pubblicazione: (2002)