Wirecube

Assembly

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Bond Assignment

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

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

Cube & Particle Tracker

No cubes yet

Assembly Overview

Total Cubes

Face-to-Face Interfaces

3

Interface Families

Interface Family Breakdown

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

Bond Assignment Settings

Dimer Overlap 4 bonds · 25% step

0%25%50%75%100%

25%

max / 4 bonds

2D Corner Overlap 8 bonds · 12.5% step

0%25%50%75%100%

25%

max / 8 bonds

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

0%25%50%75%100%

25%

max / 12 bonds

4-Face Corner Overlap 16 bonds · 6.25% step

0%25%50%75%100%

25%

max / 16 bonds

Corner scores are physically set by the Dimer slider. With d=1 bond (Dimer=25%), all corner averages ≈ 25%. With d=2 (Dimer=50%) ≈ 50%. Setting any corner slider below the dimer-implied minimum fails by pigeonhole.

Number of Random Combinations to Try Higher values increase chances of finding optimal solution but take longer

1000

Samples

Reserve V1–V4 for this assembly (hierarchical building-block mode) When checked, only V1–V4 are used for this assignment. The stage-2 assembly that uses this as a building block will then draw exclusively from V5–V8, guaranteeing zero inter-stage contamination by construction. Leave unchecked for standalone (non-hierarchical) assemblies.

Free Energy Range Filtering

Recommended Range: Loading... kcal/mol

Based on nearest neighbor stacking energies from all available bond sequences

Minimum Total Free Energy

kcal/mol

Lower bound for interface stability (sum of 4 bonds)

Maximum Total Free Energy

kcal/mol

Upper bound for interface stability (sum of 4 bonds)

Enable free energy filtering Only assign bonds with free energies in the specified range (all 4 bonds per interface must be within range)

What does this mean?

Each face-to-face interface has 4 edges, and each edge will be assigned one of 8 bond variants (V1-V8).

25% overlap means any two interfaces in the same family can share at most 1 bond (25% of 4 edges). This ensures maximum diversity between interfaces with the enlarged combinatorial space.

Free energy filtering ensures each interface (4 bonds) has a total Gibbs free energy (sum of all 4 bonds) within your specified range, based on nearest neighbor stacking energies. This helps control interface strength uniformity across the assembly.

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