DNA Origami Scaffold Selector

scaffoldselector is a computational tool for DNA origami nanostructure sequence design.

Given a particular DNA design, the program selects a scaffold sequence that minimises four classes of undesired side reactions that happen in the origami self-assembly reaction. This negative design approach allows the program to reduce kinetic traps on the folding pathway of a DNA origami, which in turn increases the probability that the scaffold strand and staple strands will self-assemble into the correct target DNA origami nanostructure.

Main use of scaffoldselector

The main use-case of the scaffoldselector is to find which sequence region of a biological vector (like a plasmid) is most suitable to use as the scaffold sequence for a particular DNA origami design. Sequences of biological origin tend to have many repeated sequence regions and are more prone to potentially problematic off-target reactions.

However, the tool can be used to select the most appropriate origami scaffold sequence from any pool of sequences desired (including pools of synthetic random sequences or De Bruijn sequences).

The scaffoldselector takes as input a contact map of your 2D or 3D origami design exported from a CAD tool, which already has all staple positions specified. caDNAno, scadnano and non-relaxed oxDNA CAD formats can all be easily converted to the contact map format.

The program proceeds to score a large pool of scaffold/staple sequence candidates which can all, in principle, Watson-Crick assemble into the target origami design. Each sequence candidate is scored according to how well it minimises four metrics, where each metric represents a category of undesired (off-target) interactions:

• Metric 1: Incorrect binding sites between staples and scaffold

• Metric 2: Intra-scaffold binding sites (where scaffold binds to itself)

• Metric 3: Staple-staple binding sites

• Metric 4: Intra-staple binding sites (where staples form hairpins)

When all metric scores are 0, the origami obeys a perfect ‘domain-level’ description: that is to say that staples only bind at intended locations on the scaffold and there are no other undesired hybridisations in the system.

However, it is often not possible to minimise all metrics to 0. Therefore, in the final step, the program selects pareto candidates which give the best trade-off in minimising all of the metrics, and an HTML report is produced containing the optimal origami sequences.

To get started using the scaffoldselector, follow the Installation instructions. Then see the Selecting Origami Scaffold as Region of a Biological Vector Sequence page for a step-by-step example.

Full technical details of our multi-objective algorithm, including experimental results which generally validate our sequence design approach for a Triangle and a Rectangle DNA origami are described in our [Journal Name] paper. If you find the scaffoldselector useful, please Cite Our Paper. Source code is available as an open source repository on Bitbucket under a MIT Licence.

As a final note, the scaffoldselector can also be used to find the optimal scaffold strand rotation for small DNA origamis that have a fixed scaffold sequence. See the Selecting Optimal Origami Scaffold Rotation page for more details.

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Contents:

• Installation
• Origami Design to Contact Map
  • scadnano to Contact Map
  • oxDNA to Contact Map
  • caDNAno to Contact Map
  • Circularising Scaffold
• Selecting Origami Scaffold as Region of a Biological Vector Sequence
  • Worked Example: DNA Fourfinger Origami
• Selecting Optimal Origami Scaffold Rotation
  • Worked Example: DNA Fourfinger Origami
  • Requirements for Scaffold Strand Rotation
• Using a Computing Cluster
  • Install Software on Cluster
  • Worked Example: DNA Origami Rectangle
  • Worked Example: DNA Origami Triangle
  • Technical Notes
• Single Origami Analysis
• Other Notes
  • Scoring on Less Metrics
  • Run Results with Less Metrics
  • DNA Origami Recommended
  • Code Optimisation
• Cite Our Paper