Coarse-grained models of DNA and RNA

Joined October 2013
51 Photos and videos
oxDNA and oxRNA retweeted
Here it is, the first bond that strengthens under stress (Nature Chemistry). Excellent work by Martijn van Galen, Annemarie Bok and Taieesa Peshkovsky, in collaboration with Joris Sprakel @GreenMechanobio and Jasper van der Gucht! @WUR @PCC_WUR @orc_wur nature.com/articles/s41557-0…
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Featuring a bit of oxDNA to characterize the DNA origami nanoswitch.
New paper alert: A pH-sensitive DNA origami nanoswitch with death receptor ligands demonstrates cytotoxicity in an acidic microenvironment, reducing breast cancer tumor growth with minimal on-target/off-tumor toxicity. nature.com/articles/s41565-0…
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oxDNA and oxRNA retweeted
Our @ox_DNA /oxRNA models are still not fast enough to capture the timescales of bulk self assembly or large nanostructure folding.A new model (ANNaMO) developed with F.Guerra,@lrovigatti,@floppleton is a step towards more coarse representations of DNA/RNA doi.org/10.1063/5.0202829

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oxDNA and oxRNA retweeted
16 May 2024
Our new paper "Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments" is just out in @ScienceMagazine ! We use multiscale modeling and optimization theory to realize one of the main goals of colloidal self-assembly, the pyrochlore lattice.🧵1/7:
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oxDNA and oxRNA retweeted
18 Mar 2024
Our new model for DNA and RNA coarse-grained simulations is now out in @JChemPhys : doi.org/10.1063/5.0199558 It is called #oxNA and includes @ox_DNA and #oxRNA models, and adds support for hybrid DNA:RNA duplexes: 🧵1/4
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oxDNA and oxRNA retweeted
Can one self-assemble containers the size of cells using a single DNA origami? Well, now we can. Check out our preprint, where we present the underlying Dipid (DNA origami inspired by lipids) framework(biorxiv.org/content/10.1101/…). (TEM image of a collapsed container)
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Featuring a little bit of oxDNA to characterize the DNA origami units: doi.org/10.1101/2024.02.09.5…

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A paper in @nanoscale_rsc featuring oxDNA simulations of the mechanisms of hybridization on DNA-coated gold nanoparticles: doi.org/10.1039/D3NR06140J

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oxDNA and oxRNA retweeted

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A combined experiment and simulation (oxDNA all-atom) preprint on how bending leads to DNA unwinding. doi.org/10.1101/2024.02.14.5…

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