oxDNA and oxRNA

Featuring a bit of oxDNA to characterize the origamis: doi.org/10.1038/s41557…

Here we report the DNA Origami Tension Sensor (DOTS) & measure TCR-pMHC forces in cell-cell junctions! Forces measured using microscopy or flow cytometry! @EmoryChem⁩ ⁦@YuesongH⁩ ⁦@salaitalab⁩ ⁦@EmoryUniversity⁩ nature.com/articles/s4156…

Featuring a little bit of oxDNA to characterize the tension sensor: doi.org/10.1038/s41565…

8y in the making and out now. Very proud of this, in collaboration with @NanoChemBiol, by fantastic phd student @galen_martijn. We managed to engineer one of Nature’s most clever molecular mechanobiology tool from the bottom up: de novo-catch bonds…a 🧵 nature.com/articles/s4155…

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/s4155…

Featuring oxDNA simulations of the catch-bond system: doi.org/10.1038/s41557…

Featuring a bit of oxDNA to characterize the DNA origami nanoswitch.

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/10.1063/5.0202…

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:

Our new model for DNA and RNA coarse-grained simulations is now out in @JChemPhys : doi.org/10.1063/5.0199… It is called #oxNA and includes @ox_DNA and #oxRNA models, and adds support for hybrid DNA:RNA duplexes: 🧵1/4

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/10.110…). (TEM image of a collapsed container)

Featuring a little bit of oxDNA to characterize the DNA origami units: doi.org/10.1101/2024.0…

Activationless Electron Transfer of Redox-DNA in Electrochemical Nanogaps | Journal of the American Chemical Society @CNRS @univ_paris_cite @UTokyo_News_en #ElectronTransfer #RedoxDNA #Nanogaps #Electrochemistry pubs.acs.org/doi/10.1021/ja…

Featuring simulations with the oxDNA model to characterize electrode-tethered redox-DNA systems: doi.org/10.1021/jacs.3…

Spacer-Programmed Two-Dimensional DNA Origami Assembly | Journal of the American Chemical Society @CHNSci #2D #DNA #Origami #Assembly pubs.acs.org/doi/10.1021/ja…

Featuring oxDNA simulations to characterize the DNA origami: doi.org/10.1021/jacs.3…

A paper in @nanoscale_rsc featuring oxDNA simulations of the mechanisms of hybridization on DNA-coated gold nanoparticles: doi.org/10.1039/D3NR06…

Featuring oxDNA simulations to characterize the DNA tetrahedra: doi.org/10.1002/smll.2…

Bending Unwinds DNA biorxiv.org/cgi/content/sh… #bioRxiv

A combined experiment and simulation (oxDNA + all-atom) preprint on how bending leads to DNA unwinding. doi.org/10.1101/2024.0…