Research-Stack/6-Documentation/docs/dna_cad_model_source_survey.md

DNA CAD / 3D-Printable Model Source Survey

Date: 2026-05-08

Purpose: identify downloadable DNA structure models that can feed the CAD force probe work. This is a source survey, not an endorsement that any model is already mechanically valid for load testing.

Best Candidates

NIH 3D: DNA Segment Based on 1BNA

Source:

https://3d.nih.gov/entries/251
https://3d.nih.gov/entries/download/251/2

Why it matters:

PDB-based DNA segment
based on 1BNA
NIH 3D output includes STL / GLB / WRL / X3D / PNG
good science-aligned starting point

Use:

baseline scientific DNA segment
geometry extraction
comparison against generated 1BNA pipeline

Hold:

likely fragile as a direct mechanical test object unless thickened or embedded

NIH 3D: Triplex and Duplex DNA Flexible Model Kits

Source:

https://3d.nih.gov/entries/22792/1
https://3d.nih.gov/entries/download/22792/1

Why it matters:

flexible kit based on 1BWG and 1BNA
includes duplex and triplex components
files include STL plus visualization formats
explicitly designed as reconfigurable model parts

Use:

best candidate for force-probe style bench tests
base-pair component load / snap-fit / connector behavior
duplex versus triplex geometry comparison

Hold:

model page recommends sintered nylon for stacks
FDM may need rescaling and connector tolerance checks

NIH 3D: DNA Playset

Source:

https://3d.nih.gov/entries/259

Why it matters:

35,000,000:1 scale DNA playset
four nucleotide parts snap together into arbitrary sequences
mechanically inspectable modular model

Use:

sequence-dependent physical assembly tests
connector tolerance / load distribution in modular DNA

Hold:

educational scale model, not atomistic force model

NIH 3D: Folding DNA Model

Source:

https://3d.nih.gov/entries/3DPX-001475

Why it matters:

modular DNA model that can be extended
single strands can separate to illustrate base pairing
includes detailed assembly and FDM printing notes

Use:

strong practical candidate for print-and-measure experiments
base-pair snap fit
strand separation
repeat-unit load path testing

Hold:

pins may break if printed in weak orientation
model may need scaling and print orientation controls

NIH 3D: Flexible ssDNA and ssRNA

Source:

https://3d.nih.gov/entries/8880

Why it matters:

teaching models of ssDNA / ssRNA in stick representation
uses PDB 1EHZ
successfully printed using laser sintering / elastomeric material per source

Use:

single-strand flexibility comparison
material-dependent bend / torsion proxy

Hold:

not a double-helix lattice by itself

Secondary Candidates

Sketchfab: DNA Stick and Ball Molecular Model

Source:

https://sketchfab.com/3d-models/dna-stick-and-ball-molecular-model-a8d959ad7f6649a784ae9a874ade7826

Why it matters:

downloadable 3D model
built in ChimeraX from PDB ID 1BNA
CC Attribution
good visual / atomistic reference mesh

Use:

visual comparison
atomistic 1BNA reference
mesh inspection

Hold:

NoAI restriction noted by source
high triangle count
may require repair / thickening for actual printing

CGTrader: DNA Double Helix Free 3D Print Model

Source:

https://www.cgtrader.com/free-3d-print-models/miniatures/other/dna-double-helix

Why it matters:

free model
STL and Rhino 3DM formats
marked prepared for 3D printing

Use:

decorative / gross double-helix geometry
possible CAD-editable Rhino route

Hold:

not necessarily PDB-derived
license and no-AI terms need review before derivative use

3DCADBrowser: B-DNA

Source:

https://www.3dcadbrowser.com/3d-model/b-dna

Why it matters:

B-DNA model
formats include STL, OBJ, FBX, BLEND, DXF, DWG, and others
atom spheres identify oxygen, nitrogen, hydrogen, carbon, phosphorus

Use:

format diversity
CAD import / conversion experiments

Hold:

download terms may require account or credits
source has spelling/metadata roughness
verify license before reuse

MakerWorld: DNA Double Helix

Source:

https://makerworld.com/en/models/437066-dna-double-helix

Why it matters:

free STL/CAD model
DNA model with support guidance

Use:

quick print sanity check
decorative helix comparison

Hold:

CC BY-NC-SA license
not scientific geometry

Printables DNA Tag

Source:

https://www.printables.com/tag/dna

Why it matters:

aggregates many DNA tagged STL models
includes folding DNA model kit, double helix models, lamps, manipulatives

Use:

candidate discovery
practical FDM variants
compare support-free versus supported helix forms

Hold:

tag page contains mixed decorative, educational, and unrelated models
vet each license and geometry manually

Generation Route

RCSB PDB / PDB-101 + NIH 3D Workflow

Sources:

https://pdb101.rcsb.org/learn/3d-printing
https://pdb101-west.rcsb.org/learn/3d-printing/pdb-structures-and-3d-printing
https://3d.nih.gov/submit

Why it matters:

RCSB PDB provides scientific source structures
PDB-101 documents 3D printing workflows
NIH 3D can process PDB / CIF and mesh files
NIH 3D can export customized GLB or STL

Recommended structure IDs:

1BNA  B-DNA dodecamer
1BWG  triplex DNA component in NIH flexible kit
1EHZ  ssDNA / ssRNA teaching model source
4UN4  Cas9 with target DNA, useful for protein-DNA complex context

Use:

generate our own controlled source mesh from PDB data
hash PDB input
hash STL / GLB output
record conversion parameters
feed into CAD force-probe receipt

Shortlist for the Force-Probe Path

Best practical order:

1. NIH 3D Folding DNA Model
2. NIH 3D Triplex and Duplex DNA Flexible Model Kits
3. NIH 3D DNA Playset
4. NIH 3D DNA Segment Based on 1BNA
5. Self-generated 1BNA model through NIH 3D or ChimeraX

Rationale:

modular and snap-fit models are better bench objects than fragile atomistic meshes
scientific 1BNA models are better for geometry truth but may need thickening
decorative helices are useful as print controls but weak as biological models

Failure Rules

decorative helix treated as scientific DNA geometry                 -> hold
PDB-derived mesh treated as mechanically printable without repair   -> hold
license omitted from candidate selection                            -> invalid source record
downloaded STL used without hash / provenance                       -> invalid receipt
atomistic visual mesh used as load-bearing model without thickening  -> unsafe / invalid