Coarse-grained models of DNA and RNA
Oxford
Joined October 2013
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Featuring a bit of oxDNA to characterize the origamis: doi.org/10.1038/s41557-024-0…
oxDNA and oxRNA retweeted
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/s41565-0…
Featuring a little bit of oxDNA to characterize the tension sensor: doi.org/10.1038/s41565-024-0…
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…
Featuring oxDNA simulations of the catch-bond system: doi.org/10.1038/s41557-024-0…
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…
ALT a, A three-dimensional origami has a head part with a cavity that physically hides six peptide ligands conjugated to DNA strands. b, Illustration of the mechanism of how a peptide ligand hides inside the head cavity via the entropic spring imparted by the random coiling of the TFO. c, When the pH drops, the TFO of the peptide–DNA conjugate forms a tsDNA that forces the six peptides that were originally hidden in the cavity to get displayed as a hexagonal pattern on the top surface of the origami. d, Close-ups of the tsDNA. Wang, Y., Baars, I., Berzina, I. et al. A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns. Nat. Nanotechnol. (2024). https://doi.org/10.1038/s41565-024-01676-4
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
oxDNA and oxRNA retweeted
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:
oxDNA and oxRNA retweeted
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
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)
Featuring a little bit of oxDNA to characterize the DNA origami units:
doi.org/10.1101/2024.02.09.5…
oxDNA and oxRNA retweeted
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/jac…
Featuring simulations with the oxDNA model to characterize electrode-tethered redox-DNA systems:
doi.org/10.1021/jacs.3c13532
oxDNA and oxRNA retweeted
Spacer-Programmed Two-Dimensional DNA Origami Assembly | Journal of the American Chemical Society @CHNSci #2D #DNA #Origami #Assembly pubs.acs.org/doi/10.1021/jac…
Featuring oxDNA simulations to characterize the DNA origami:
doi.org/10.1021/jacs.3c13180
A paper in @nanoscale_rsc featuring oxDNA simulations of the mechanisms of hybridization on DNA-coated gold nanoparticles:
doi.org/10.1039/D3NR06140J
Featuring oxDNA simulations to characterize the DNA tetrahedra:
doi.org/10.1002/smll.2023091…
oxDNA and oxRNA retweeted
Bending Unwinds DNA biorxiv.org/cgi/content/shor… #bioRxiv
A combined experiment and simulation (oxDNA + all-atom) preprint on how bending leads to DNA unwinding.
doi.org/10.1101/2024.02.14.5…
A preprint with a bit of oxDNA to characterize the gated DNA origami nanopores:
doi.org/10.21203/rs.3.rs-387…