oxDNA and oxRNA

Coarse-grained models of DNA and RNA

[oxDNA and oxRNA @ox_DNA]

Featuring a bit of oxDNA to characterize the origamis: https://t.co/QlsnYcUsgg

[Khalid Salaita @k_salaita]

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 https://t.co/XmDnPKD6ZV

[oxDNA and oxRNA @ox_DNA]

Featuring a little bit of oxDNA to characterize the tension sensor: https://t.co/IlOBUl0oRz

[Albada Lab @NanoChemBiol]

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

https://t.co/BkFn2mEjvd

[oxDNA and oxRNA @ox_DNA]

Featuring oxDNA simulations of the catch-bond system: https://t.co/CUnhB7WarJ

[oxDNA and oxRNA @ox_DNA]

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

[Nature Nanotechnology @NatureNano]

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.
https://t.co/PWCKVkOMQh

[Petr Šulc @petr_sulc]

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
https://t.co/cpnJu1mFEW

[Petr Šulc @petr_sulc]

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:

[Petr Šulc @petr_sulc]

Our new model for DNA and RNA coarse-grained simulations is now out in @JChemPhys :
https://t.co/FapnoqG8ES
It is called #oxNA and includes @ox_DNA and #oxRNA models, and adds support for hybrid DNA:RNA duplexes:
🧵1/4

[Christoph Karfusehr @karfusehr]

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(https://t.co/oaUOybQzXC).

(TEM image of a collapsed container)

[oxDNA and oxRNA @ox_DNA]

Featuring a little bit of oxDNA to characterize the DNA origami units:
https://t.co/kNcwbHPfFN

[J. Am. Chem. Soc. @J_A_C_S]

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 https://t.co/Erc6MbbTgZ

[oxDNA and oxRNA @ox_DNA]

Featuring simulations with the oxDNA model to characterize electrode-tethered redox-DNA systems:
https://t.co/NzS2YWmCn1

[J. Am. Chem. Soc. @J_A_C_S]

Spacer-Programmed Two-Dimensional DNA Origami Assembly | Journal of the American Chemical Society @CHNSci #2D #DNA #Origami #Assembly https://t.co/Mya73VlljD

[oxDNA and oxRNA @ox_DNA]

Featuring oxDNA simulations to characterize the DNA origami:
https://t.co/GHaaf3mCku

[oxDNA and oxRNA @ox_DNA]

A paper in @nanoscale_rsc featuring oxDNA simulations of the mechanisms of hybridization on DNA-coated gold nanoparticles:
https://t.co/NOyqrV8gox

[oxDNA and oxRNA @ox_DNA]

Featuring oxDNA simulations to characterize the DNA tetrahedra:
https://t.co/ba17ldBi20

[bioRxiv @biorxivpreprint]

Bending Unwinds DNA https://t.co/iVi1sMwm1c #bioRxiv

[oxDNA and oxRNA @ox_DNA]

A combined experiment and simulation (oxDNA + all-atom) preprint on how bending leads to DNA unwinding.
https://t.co/FrFqb4xHEy

[oxDNA and oxRNA @ox_DNA]

A preprint with a bit of oxDNA to characterize the gated DNA origami nanopores:
https://t.co/QFhcLbLpBW