# DnaOS — DNA Origami Studio

> DnaOS is a free, open-source (GPL-3.0) web app for designing DNA origami and DNA double-crossover (DX) tiles. Everything runs in the browser: designs, sequences, and exports stay on the user's computer.

DnaOS is made by Abhishek Kumar. It covers the whole design loop: draw a shape, route the scaffold and staples, check the result, and export what a lab needs to order and simulate.

## Main pages

- [Home](/): starting points, a shape library (including designs recreated from published papers), and how the studio works
- [Origami studio](/studio): honeycomb and square lattice design, 3D wireframe cages and tubes, routing, cargo, equilibration, and exports
- [DX tile designer](/dae): DAE and DAO double-crossover molecules and A/B lattices, sequence generation, and stability checks
- [DAE 3D viewer](/dae/viewer): view and edit nucleotide-level structures, and open oxDNA and oxView files
- [Cite DnaOS](/cite): how to cite DnaOS, with APA and BibTeX

## What the origami studio does

- Paint helices on a honeycomb or square lattice cross-section or silhouette, or paint and erase directly in 3D
- Build 3D wireframe cages (polyhedra, rings, cylinders) with 2-helix or thicker bundles per edge
- Route the scaffold (M13mp18 and others) and break staples to lattice crossover rules
- Edit the path map: break, join, add crossovers, and skip bases
- Place cargo (proteins from the Protein Data Bank, dyes, biotin, and click-chemistry handles) on staple ends
- Relax the structure with a bead model, run on the GPU (WebGPU) for large designs
- Colour schemes for figures, including colour-blind-safe and greyscale options
- Export: staple order CSV with modifications, design JSON (caDNAno-compatible import), 2D route SVG, oxDNA topology and configuration, GLB 3D models for Blender, and print-resolution images

## What the DX tile designer does

- Design DAE and DAO molecules with even or odd half-turns between crossovers, sticky ends, hairpins, and end labels
- Build DAE-O and DAO-E A/B lattices
- Score every strand–strand domain with nearest-neighbour thermodynamics at the user's temperature, Mg²⁺, and EDTA
- Estimate annealing and report crossover twist
- Export FASTA, order CSV, and oxDNA files

## Science and data

- Lattice geometry and crossover spacing follow the caDNAno conventions (Douglas et al., Nucleic Acids Res. 2009): 10.5 bp per turn, 0.34 nm rise
- Duplex stability uses SantaLucia (1998) nearest-neighbour parameters
- Protein structures come from the RCSB Protein Data Bank; small molecules from PubChem
- Parts of the DAE 3D viewer are adapted from oxView (Šulc group, GPL-3.0)

## Optional

- [Privacy policy](/privacy)
- [Terms and conditions](/terms)
- [License (GPL-3.0)](/license)
- [Third-party attribution](/attribution)