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...

Bibliográfalaš dieđut
Váldodahkkit:	Ratajczyk, EJ, Šulc, P, Turberfield, AJ, Doye, JPK, Louis, AA
Materiálatiipa:	Internet publication
Giella:	English
Almmustuhtton:	2023

Geahča maid

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Sequence-dependent thermodynamics of a coarse-grained DNA model.
Dahkki: Šulc, P, et al.
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Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling
Dahkki: Doye, JPK, et al.
Almmustuhtton: (2022)

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

Coarse-graining DNA for simulations of DNA nanotechnology.
Dahkki: Doye, J, et al.
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Coarse-Grained Modelling of Extreme DNA Bending
Dahkki: Harrison, R, et al.
Almmustuhtton: (2014)

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

DNA nanotweezers studied with a coarse-grained model of DNA
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Modelling toehold-mediated RNA strand displacement
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Coarse-grained simulations of DNA overstretching.
Dahkki: Romano, F, et al.
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Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
Dahkki: Ouldridge, T, et al.
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Coarse-grained modelling of the structural properties of DNA origami
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Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
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Coarse-grained modelling of nucleic acids
Dahkki: Sulc, P
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Dahkki: Sharma, R, et al.
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Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
Dahkki: Schreck, J, et al.
Almmustuhtton: (2016)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Simulating large DNA nanostructures with a coarse-grained model
Dahkki: Snodin, B
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DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
Dahkki: Schreck, J, et al.
Almmustuhtton: (2014)

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Dahkki: Sampsa Vierros, et al.
Almmustuhtton: (2019-09-01)

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
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Almmustuhtton: (2019-10-01)

Influence of ionic conditions on knotting in a coarse-grained model for DNA
Dahkki: Sarah Wettermann, et al.
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Coarse-graining polymers as soft colloids
Dahkki: Louis, A, et al.
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