Wirecube

Assembly

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Tools

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Bond Assignment

Assign DNA bonds to face-to-face interfaces. Sign in to use bond assignment and plates.

DNA-PAINT

Visualize vacant extension sites as docking strands. Upload an image to rasterize probe patterns. Assign Exchange-PAINT rounds.

Saved Designs

No saved designs yet. Click "Save" to save your current design.

Assembly Name

X Cubes

cubes

Y Cubes

cubes

Z Cubes

cubes

Building Block (hierarchical stage 2)

Assembly Style

Edit Mode

Total Cubes

8

cubes

Total Edges

96

edges

Total Vertices

64

vertices

Assembly Volume

1000000

nm³

Hex Blocks

2

hexamers

Efficiency

22

% filled

Bond Quality

— —

Assign bonds to score

Assembly Properties

Dimensions (X×Y×Z)	2×2×2
Assembly Style	Diagonal Corner Touch

Structural Analysis

DNA Strand Length	~2,400 nt
Assembly Complexity	Moderate
Folding Temperature	37°C
Estimated Yield	85%

Plate Management System

How to use: Design your cube assembly, assign bonds, then click "Add to Plate" in the sidebar to add it to the current plate. Each cube uses approximately 169 DNA sequences (145 core + 24 bond sequences).

All Plates

No plates yet

Plate Name: -

Plate Type: -

Wells Used: 0

Total Sequences: 0

Well Grid

Universal scaffold

Create a plate to get started

Assembly Overview

Total Cubes

Face-to-Face Interfaces

3

Interface Families

Interface Family Breakdown

Family	Interface Type	Count
Family 1	Right-Left (X-axis)	0
Family 2	Top-Bottom (Z-axis)	0
Family 3	Front-Back (Y-axis)	0

Bond Assignment Settings

Simulated annealing

Rearranges bond words to remove multi-face traps

Annealing effort

Bonds per Interface

Per interaction

1 2 3 4

spread the empty edge of 3-bond faces

Extended bond library (V1–V16) 16 variants / bond

Off by default (uses V1–V8). When on, assignment draws from 16 orthogonal sticky-end variants per bond — more options mean fewer parasitic reuses, so larger structures score higher. V9–V16 ship from the F2F_V9_V16 source plate.

Dimer Overlap Range 4 bonds · 25% step

0%25%50%75%100%

≤25%

of 4 bonds

2D Corner Overlap Range 8 bonds · 12.5% step

0%25%50%75%100%

≤25%

of 8 bonds

3-Face Corner Overlap Range 12 bonds · ≈8.3% step

0%25%50%75%100%

≤25%

of 12 bonds

4-Face Corner Overlap Range 16 bonds · 6.25% step

0%25%50%75%100%

≤25%

of 16 bonds

Free Energy Window

— kcal/mol

0 80

Assembly Information

Cubes (Monomers)

Sequences per Cube

Total Sequences

Dimensions

Plate Selection

Select Target Plate

Auto-fill across multiple plates Automatically create additional plates if needed (for structures > 96 cubes)

Concentration & Volume Settings

Scaffold Concentration

nM

Excess Staples

×

Target = excess × scaffold

Final Volume

μL

Calculated Target Conc.

nM

Initial Staple Concentration (Stock)

μM

Source concentration from mother plate (used if concentration data is missing)

Well Assignment

Each cube will be placed in a separate well. Specify destination wells below or use auto-fill.

#	Cube ID	Target Plate	Destination Well	Status