78 research outputs found
Coarse-grained modelling of supercoiled RNA
We study the behaviour of double-stranded RNA under twist and tension using
oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit
salt-dependence into the model allows us to directly compare our results to
data from recent single-molecule experiments. The model reproduces extension
curves as a function of twist and stretching force, including the buckling
transition and the behaviour of plectoneme structures. For negative
supercoiling, we predict denaturation bubble formation in plectoneme end-loops,
suggesting preferential plectoneme localisation in weak base sequences. OxRNA
exhibits a positive twist-stretch coupling constant, in agreement with recent
experimental observations.Comment: 8 pages + 5 pages Supplementary Materia
Sequence-dependent thermodynamics of a coarse-grained DNA model
We introduce a sequence-dependent parametrization for a coarse-grained DNA
model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134,
085101 (2011)] originally designed to reproduce the properties of DNA molecules
with average sequences. The new parametrization introduces sequence-dependent
stacking and base-pairing interaction strengths chosen to reproduce the melting
temperatures of short duplexes. By developing a histogram reweighting
technique, we are able to fit our parameters to the melting temperatures of
thousands of sequences. To demonstrate the flexibility of the model, we study
the effects of sequence on: (a) the heterogeneous stacking transition of single
strands, (b) the tendency of a duplex to fray at its melting point, (c) the
effects of stacking strength in the loop on the melting temperature of
hairpins, (d) the force-extension properties of single strands and (e) the
structure of a kissing-loop complex. Where possible we compare our results with
experimental data and find a good agreement. A simulation code called oxDNA,
implementing our model, is available as free software.Comment: 15 page
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\unicode{x2014}oxDNA
and oxRNA. The model naturally reproduces the physical properties of hybrid
duplexes including their structure, persistence length and force-extension
characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we
fit the model's thermodynamic properties to experimental data using both
average-sequence and sequence-dependent parameters. To demonstrate the model's
applicability we provide three examples of its use\unicode{x2014}calculating
the free energy profiles of hybrid strand displacement reactions, studying the
resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.Comment: 15 pages, 10 figure
Symmetries of finite Heisenberg groups for k-partite systems
Symmetries of finite Heisenberg groups represent an important tool for the
study of deeper structure of finite-dimensional quantum mechanics. This short
contribution presents extension of previous investigations to composite quantum
systems comprised of k subsystems which are described with position and
momentum variables in Z_{n_i}, i=1,...,k. Their Hilbert spaces are given by
k-fold tensor products of Hilbert spaces of dimensions n_1,...,n_k. Symmetry
group of the corresponding finite Heisenberg group is given by the quotient
group of a certain normalizer. We provide the description of the symmetry
groups for arbitrary multipartite cases. The new class of symmetry groups
represents very specific generalization of finite symplectic groups over
modular rings.Comment: 6 pages, to appear in Proceedings of QTS7 "Quantum Theory and
Symmetries 7", Prague, August 7-13, 201
On the biophysics and kinetics of toehold-mediated DNA strand displacement
Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems
Summary of OSQAR First Achievements and Main Requests for 2008
Abstract - In the first paragraph, OSQAR foremost achievements are summarised together with a brief reminder of its scientific context. In the second paragraph, activities planned for 2008 are briefly reviewed including the expected scientific results. The third paragraph is devoted to the requests addressed to CERN as the host laboratory and as a collaboration member of the OSQAR photon regeneration experiment
A nucleotide-level coarse-grained model of RNA
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (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 modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na +] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA
- …