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...

Πλήρης περιγραφή

Λεπτομέρειες βιβλιογραφικής εγγραφής
Κύριοι συγγραφείς:	Ratajczyk, EJ, Šulc, P, Turberfield, AJ, Doye, JPK, Louis, AA
Μορφή:	Internet publication
Γλώσσα:	English
Έκδοση:	2023

Παρόμοια τεκμήρια

Coarse-grained modeling of DNA and DNA nanotechnology
ανά: Ouldridge, T, κ.ά.
Έκδοση: (2012)

Coarse-grained modelling of supercoiled RNA
ανά: Matek, C, κ.ά.
Έκδοση: (2015)

A nucleotide-level coarse-grained model of RNA
ανά: Šulc, P, κ.ά.
Έκδοση: (2014)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
ανά: Šulc, P, κ.ά.
Έκδοση: (2014)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
ανά: Sulc, P, κ.ά.
Έκδοση: (2012)

Sequence-dependent thermodynamics of a coarse-grained DNA model.
ανά: Šulc, P, κ.ά.
Έκδοση: (2012)

Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling
ανά: Doye, JPK, κ.ά.
Έκδοση: (2022)

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
ανά: Ouldridge, T, κ.ά.
Έκδοση: (2013)

Coarse-graining DNA for simulations of DNA nanotechnology.
ανά: Doye, J, κ.ά.
Έκδοση: (2013)

Coarse-Grained Modelling of Extreme DNA Bending
ανά: Harrison, R, κ.ά.
Έκδοση: (2014)

DNA nanotweezers studied with a coarse-grained model of DNA.
ανά: Ouldridge, T, κ.ά.
Έκδοση: (2010)

DNA nanotweezers studied with a coarse-grained model of DNA
ανά: Ouldridge, T, κ.ά.
Έκδοση: (2010)

Modelling toehold-mediated RNA strand displacement
ανά: Šulc, P, κ.ά.
Έκδοση: (2015)

Coarse-grained simulations of DNA overstretching.
ανά: Romano, F, κ.ά.
Έκδοση: (2013)

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
ανά: Ouldridge, T, κ.ά.
Έκδοση: (2011)

Coarse-grained modelling of the structural properties of DNA origami
ανά: Snodin, B, κ.ά.
Έκδοση: (2019)

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
ανά: Snodin, B, κ.ά.
Έκδοση: (2015)

Coarse-grained modelling of nucleic acids
ανά: Sulc, P
Έκδοση: (2014)

Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
ανά: Sharma, R, κ.ά.
Έκδοση: (2017)

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
ανά: Schreck, J, κ.ά.
Έκδοση: (2016)

Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model
ανά: Harrison, R, κ.ά.
Έκδοση: (2019)

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
ανά: Fonseca, P, κ.ά.
Έκδοση: (2018)

Measuring internal forces in single-stranded DNA: application to a DNA force clamp
ανά: Engel, MC, κ.ά.
Έκδοση: (2020)

The interplay of supercoiling and thymine dimers in DNA
ανά: Lim, W, κ.ά.
Έκδοση: (2022)

Force-induced rupture of a DNA duplex: from fundamentals to force sensors
ανά: Mosayebi, M, κ.ά.
Έκδοση: (2015)

TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami
ανά: Suma, A, κ.ά.
Έκδοση: (2019)

Bottom-up coarse-grained modeling of DNA
ανά: Sun, Tiedong, κ.ά.
Έκδοση: (2021)

DNA hybridization kinetics: zippering, internal displacement and sequence dependence.
ανά: Ouldridge, T, κ.ά.
Έκδοση: (2013)

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

The free-energy landscape of a mechanically bistable DNA origami
ανά: Wong, CK, κ.ά.
Έκδοση: (2022)

Designing the self-assembly of arbitrary shapes using minimal complexity building blocks
ανά: Bohlin, J, κ.ά.
Έκδοση: (2023)

Direct simulation of the self-assembly of a small DNA origami
ανά: Snodin, BEK, κ.ά.
Έκδοση: (2016)

Coarse-grained (hybrid) integrative modeling of biomolecular interactions
ανά: Jorge Roel-Touris, κ.ά.
Έκδοση: (2020-01-01)

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

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

DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
ανά: Schreck, J, κ.ά.
Έκδοση: (2014)

Hybrid Atomistic and Coarse-Grained Model for Surfactants in Apolar Solvents
ανά: Sampsa Vierros, κ.ά.
Έκδοση: (2019-09-01)

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing
ανά: Rodrigo V. Honorato, κ.ά.
Έκδοση: (2019-10-01)

Influence of ionic conditions on knotting in a coarse-grained model for DNA
ανά: Sarah Wettermann, κ.ά.
Έκδοση: (2023-01-01)

Coarse-graining polymers as soft colloids
ανά: Louis, A, κ.ά.
Έκδοση: (2002)