DnaOSηα

DnaOS (DNA Origami Studio) is a free browser studio for geometric design of DNA nanostructures. The origami studio places honeycomb or square lattice helices as cages, tubes, filled solids, flat pictures, and letters. A separate DAE designer builds antiparallel DNA double-crossover molecules (DX tiles: DAE, DAO, DAE-O). Designs stay in this browser until you export files.

Lattice-origami and 3D-bundle editors already exist, and many published designs still begin there. They can also take a long stretch of tutorials and interface time before a first cage or lattice appears. DnaOS is a smaller, browser-first studio: pre-loaded shapes, a short walkthrough, and hover hints on the buttons. It is for students and researchers who want to try a geometry or an idea without a long setup.

People learning scaffolded DNA origami (Rothemund 2006; Douglas honeycomb 2009), wireframe cages, honeycomb barrels, or Fu–Seeman DX tiles — and people who already know the field and want a quick sketch of a new shape. Use a computer or laptop with a mouse or trackpad. Phones are not a supported layout.

No. DnaOS is a browser sketch for honeycomb or square lattices, a two-rail helix path, in-browser 3D cages and tubes, cargo tags, a download pack, and a DAE/DX workbench. If a paper already has a lattice or 3D-bundle pipeline, keep that pipeline; DnaOS can still help you explore a shape first.

No. Foundations lists methods papers so you can cite the science, not because DnaOS is an official product of those laboratories. Cite DnaOS separately if the studio helped a figure or thesis.

On Home → Start: Place rods (empty 3D canvas), blank honeycomb, blank square lattice, open a DnaOS or helix-lattice JSON, or resume the last browser session. Or click a pre-loaded cage, tube, lattice picture, letter, or a DAE / DX tile example. Walkthrough is three steps: pick a cage, edit in 3D, Route.

A current desktop or laptop browser with WebGL (Chrome, Edge, Firefox, or Safari), JavaScript on, and a mouse or trackpad. Large geodesic cages and thick bundles after Route prefer about 16 GB RAM and a working GPU. Designs are not computed on a DnaOS server.

In this browser until you export. Save JSON or a download pack if you need a copy on disk. Clearing site data forgets the session.

B-DNA: 2 nm helix diameter, 0.34 nm rise per base pair, ~10.5 bp/turn, and 2.5 nm lattice spacing between neighboring helices. Cage edges and lattice lengths are in base pairs. These are standard structural-DNA defaults, not a fitted crystal structure of your design.

Wireframe 3D cages (tetrahedron, cube, octahedron, geodesic balls, and more) whose edges are DNA helix bundles that meet at vertices. Honeycomb nanotubes and multilayer barrels. Filled lattice solids and flat 2D pictures (including letters). You can also click-drag DNA rods in empty space. This is scaffolded origami on a lattice or a cage graph — not a tile array and not a single DX molecule.

Route lays a scaffold through occupied helices (centroid-rooted Prim spanning tree) and then autostaples. That is a design heuristic so the path map has a continuous scaffold plus staple oligos. It is not a prediction of folding yield. After Route, open Path (shortcut P) to nick, join, and add crossovers.

A two-rail helix diagram: both strands of each helix, U-turns, crossovers, and 5′/3′ ends — not a single colored line. You can break, ligate, and draw crossovers, then download the 2D route as SVG or include it in the zip pack. Staple sequences appear beside the path for ordering.

A short in-browser spring pass: backbone bonds, base-pair springs, and excluded volume, with a step cap. It eases obvious clashes in the 3D view. It is not molecular dynamics. Export coarse-grained .top/.dat if you need a full MD run.

Honeycomb is the usual 3D origami packing (Douglas et al., 2009): six neighbors, ~2.5 nm spacing. Square is four-neighbor packing, often used for flat sheets and letters. Blank honeycomb and blank square are empty canvases you paint in Cross-section or sculpt in 3D.

Vertices are joints in space; edges become DNA bundles (you set helix count and edge length in bp). Drag joints, add or delete vertices, delete one helix from a bundle, then Route. Extrude vs sweep changes whether corners stay sharp. Bundle thickness of 2 helices is often recommended so one M13 scaffold can cover a cage.

Parallel helices packed as concentric honeycomb rings (6, 18, 30 … helices; ring n has 6(2n − 1)). Inner ring 1 is the 6-helix nanotube; 2 or more leaves a wider bore. You can keep a half-pipe or quarter shell, then bake into a lattice you can still paint.

Default is M13mp18 / p7249 (7249 nt), the common single-stranded scaffold for origami. p7560 and p8064 names exist as length checks; their full sequences are not shipped. Custom scaffold is a length you type. Staples are assigned from the scaffold path after Route. Always check staple length and scaffold usage before ordering.

Optional wet-lab tags on staples: peptides (NHS-amide, or a hanging ssDNA handle for ssDNA–peptide conjugates via maleimide–thiol), antibodies/nanobodies (hybridization handles), proteins (e.g. 5′ DBCO), nanoparticles and dyes, nucleic acids and drugs, lipids, azide/DBCO click, intercalators, and opening (cut-window) sites. Handles, antihandles, and terminal-modification codes are written into the staple CSV. DnaOS does not conjugate the cargo for you.

Yes. Cross-section paints or erases helices on the honeycomb or square map. 3D sculpt brushes add or remove occupied sites like clay. Silhouette fill stamps a 2D picture through the stack. Then Route.

An empty 3D canvas. Click-drag to place DNA bundles between joints you create, without starting from a named polyhedron. Useful for a custom wireframe.

DAE means double crossover, antiparallel, even half-turns between two Holliday junctions (Fu & Seeman, Biochemistry 1993). Two B-DNA helices are fused on the inner strand pair. Antiparallel DX tiles (DAE and DAO) are rigid bricks of structural DNA nanotechnology; parallel DX molecules usually are not. This is not scaffolded origami.

DAE: even number of half-turns between the two crossovers (often 4 × 10.5 bp ≈ 21 bp). DAO: odd half-turns. DAE-O: a DAE with sticky-end overhangs so tiles can form 2D arrays (Winfree et al.). Home examples load Isolated DAE, Fu–Seeman DAE, DAE-O, and DAO into the designer.

No. /dae is an independent molecule editor: add strands or duplexes, pair, nick, ligate, sticky ends, Holliday crossovers, delete a helix, and rotate/tilt helices (including 60° in-plane turns). The origami studio does not open a DAE file as a cage. Shared science is B-DNA geometry and DX literature, not a shared document.

An in-app coarse-grained 3D canvas for the current DAE molecule: orbit, select, translate, rotate, nick, ligate, pair, crossover, relax toward B-DNA, screenshot, save structure JSON, and .top/.dat. An external GPU MD viewer can open those files in a new tab.

No. The DAE designer copies FASTA so you can paste it into an external calculator. Helix occupancy here uses a two-state SantaLucia nearest-neighbor estimate (25 °C proxy), not a multi-complex partition function.

Yes in the DAE designer. Roll the groove, turn a helix in the screen plane (15° or 60°), and tilt toward or away from the camera. That is a geometric construction aid, not a one-click multi-ring or 3D-bundle preset.

Origami studio: DnaOS JSON, two-rail path SVG, staple CSV (with cargo mods), cargo CSV, oligo-order CSV, FASTA, coarse-grained .top/.dat, cage XYZ, then a 3D image as SVG, PNG, TIFF, and a GLB model for Blender or BioDiorama, plus a zip pack (route + 3D PNG + order CSV + staples + FASTA + cargo when present). DAE designer: JSON, FASTA, order CSV, .top/.dat, structure JSON, path PNG, 3D PNG. Order-CSV columns are Name, Sequence, Scale (25 nmole), Purification (STD).

Home → Open design JSON and studio File → Open accept DnaOS JSON and vstrand helix-lattice files. Round-trip is best-effort. Always inspect the path after import.

Unknown until you fold it. DnaOS does not run a folding simulation, does not guarantee unique routing, and does not replace AFM, gel, or TEM. Check staple lengths, scaffold usage, nick positions, and steric clashes. Equilibration and SantaLucia screens are estimates.

No. Export CSVs and upload them to an oligo vendor. Check staple sequences and modification codes before you order.

Cite DnaOS (APA and BibTeX on Cite DnaOS, Version 2.1). Cite a methods paper from Foundations when that method is central — origami, honeycomb, cages, DX tiles, SantaLucia Tm, coarse-grained MD, Prim routing.

Email analysemydata.in@gmail.com for feedback, bug reports, source requests, and other questions. Say what you clicked, the browser, and whether it was the origami studio or the DAE designer. A JSON export or a screenshot of the 3D/path view helps. Please try a computer or laptop first — the UI is not built for a phone.