Track: Biosecurity

Difficulty: Advanced

A tool that, given an oligo pool of any size, will detect collections

of oligos in that pool that could be assembled via restriction, PCA or

Gibson-like methods. This would be an important contribution to

biosecurity around ensuring oligo pools cannot be misused to assemble

sequences that would otherwise be controlled.

1. Background and Motivation (for synthetic biologists):

In the field of synthetic biology, researchers often work with gene-length DNA sequences. Gene synthesis companies conduct sequence screening on orders for gene-length sequences to determine potential risk for misuse. However, researchers can also assemble gene-length DNA from oligo pools containing short DNA fragments. Assembling oligos in specific combinations can lead to the creation of genetic sequences with diverse applications from protein expression to genome editing. However, the use of oligo pools to assemble gene-length sequences could also be used to bypass biosecurity screening protocols. To address this concern, there is a need for a specialized tool that can detect collections of oligos within a pool that could be assembled using various methods like restriction, Polymerase Chain Assembly (PCA), or Gibson-like methods, thereby extending existing biosecurity screening tools and reducing the risk of misuse of DNA.

2. Problem Statement:

The problem at hand is to design and develop an open-source software tool capable of analyzing an oligo pool of any size and identifying potential combinations of oligos in that pool that could be assembled using restriction, PCA, Gibson-like methods or other assembly protocol. This tool aims to enhance biosecurity by ensuring that oligo pools cannot be exploited to assemble sequences that might pose risks or otherwise be subject to regulatory control.

Requirements:

a) Oligo Pool Analysis: The tool should be able to analyze an input oligo pool of any size, containing DNA fragments of varying lengths and sequences. DNA synthesis providers routinely provide oligo pools from dozens to millions of unique oligo sequences in a single pool.

b) Detection of Assembly-Capable Oligos: The tool should identify collections of oligos within the pool that could be assembled using methods such as restriction, PCA, or Gibson-like methods along with the experimental conditions required for such assembly.

c) Method-Specific Algorithms: The tool should utilize specific algorithms and methods suitable for each assembly technique to accurately predict potential combinations. Potential assembly products should be scored based on the consistency of the thermodynamic properties of relationships between oligos in the pool. E.g. in a pool of oligos, if a pair of oligos would bind with a Tm of 50C but a separate pair would have a Tm of only 25C, the probability that these two pairs would come together in a single assembly would be lower than if the second pair had a Tm of 51C.