The effect of topology on the structure and free energy landscape of DNA kissing complexes.

@article{Romano2012TheEO,
  title={The effect of topology on the structure and free energy landscape of DNA kissing complexes.},
  author={Flavio Romano and Alexander Hudson and Jonathan P. K. Doye and Thomas E. Ouldridge and Ard A. Louis},
  journal={The Journal of chemical physics},
  year={2012},
  volume={136 21},
  pages={
          215102
        }
}
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0, or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the… 

Figures from this paper

Characterizing the bending and flexibility induced by bulges in DNA duplexes.
TLDR
The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures.
DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures
TLDR
The vertices of DNA tetrahedrons with DNA stem-loop sequences functionalized with variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes, which make them an important tool for DNA nanotechnology.
DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization
TLDR
The results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.
Sequence-dependent thermodynamics of a coarse-grained DNA model.
TLDR
A sequence-dependent parametrization for a coarse-grained DNA model originally designed to reproduce the properties of DNA molecules with average sequences is introduced, able to fit parameters to the melting temperatures of thousands of sequences.
Direct Simulation of the Self-Assembly of a Small DNA Origami.
By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in
A nucleotide-level coarse-grained model of RNA.
TLDR
A new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA is presented, arguing 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 Pair.
DNA hybridization kinetics: zippering, internal displacement and sequence dependence
TLDR
This work explores DNA oligomer hybridization kinetics using a coarse-grained model and explains why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and how association rates can be modulated by sequence choice.
Design principles for rapid folding of knotted DNA nanostructures
Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded
On the biophysics and kinetics of toehold-mediated DNA strand displacement
TLDR
This work 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 to provide a biophysical explanation of strand displacement kinetics.
Molecular Dynamics Study of Supercoiled DNA Minicircles Tightly Bent and Supercoiled DNA in Atomistic Resolution
TLDR
Atomic representation of supercoiled 336 base pairs minicircles was provided by fitting the DNA structure obtained by explicitly solvated MD simulations into the density maps from electron cryo-tomography, showing the effects from some subtle structural characteristics of DNA on defect formation.
...
1
2
3
...

References

SHOWING 1-10 OF 60 REFERENCES
Topological constraints in nucleic acid hybridization kinetics
TLDR
Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands.
Unusual mechanical stability of a minimal RNA kissing complex
TLDR
The strong mechanical stability of even a minimal kissing complex indicates the importance of such loop–loop interactions in initiating and stabilizing RNA dimers in retroviruses.
Coarse-Grained Modelling of DNA and DNA Self-Assembly
TLDR
The model is the first in which an explicit stacking transition is present in single strands, and also the only coarse-grained model to date to capture both hairpin formation within a single strand and duplex formation between strands.
Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semiflexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical
DNA nanotweezers studied with a coarse-grained model of DNA.
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands, duplex hybridization, single-stranded stacking, and hairpin formation, and also
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
TLDR
The structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers are explored, resulting in an "average base" description of DNA.
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.
Explicit solvent molecular dynamics (MD) simulations were carried out for three RNA kissing-loop complexes. The theoretical structure of two base pairs (2 bp) complex of H3 stem-loop of Moloney
PX DNA triangle oligomerized using a novel three-domain motif.
TLDR
This work reports the formation of a triangular species that has four strands per edge, held together by PX interactions, and demonstrates by nondenaturing gel electrophoresis and by atomic force microscopy that these triangles can be self-assembled into a linear array.
...
1
2
3
4
5
...