For the Nonaworks23 biohackathon, working on Twist problem 1: "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."
Oligonucleotides, the fundamental building blocks of genetic information, hold a pivotal role in regulating gene and protein expression, driving innovation in synthetic biology. While they offer immense potential, ensuring biosecurity in their use is imperative. Biosecurity encompasses a range of measures to safeguard the handling, storage, and distribution of these molecules, given their wide-ranging applications in molecular biology research, diagnostics, and therapeutics. However, oligonucleotides also carry biosecurity risks if mishandled or misused.
In response to these challenges, a multifaceted approach has emerged. An open-source software tool has been developed to analyze oligonucleotide pools for potential sequence combinations, allowing for their assembly using various methods while bolstering biosecurity. Furthermore, an efficient oligonucleotide preparation method, known as thermodynamically balanced, inside-out (TBIO) PCR-based assembly, has been introduced to advance the field.
In addition to these advancements, two distinct techniques for DNA manipulation play key roles. Restriction enzyme-based DNA fragmentation and reordering enable the precise cleaving of DNA at specific sites, creating fragments with compatible ends that can be seamlessly joined to form new sequences. Conversely, Gibson Assembly, or Gibson-like techniques, provide an innovative approach to joining DNA fragments without the need for restriction enzymes. By relying on overlapping sequences at the ends of DNA fragments, these methods harness a cocktail of enzymes, including DNA polymerase, exonuclease, and DNA ligase, to seamlessly and efficiently assemble DNA fragments. This approach simplifies complex DNA manipulations and offers flexibility compared to traditional restriction enzyme-based cloning methods.
Together, these techniques and tools allow researchers to harness the vast potential of oligonucleotides while ensuring their secure and responsible use in the field of biology and synthetic biology.
Presentation link: https://docs.google.com/presentation/d/15woLU7qLoDPnVbCyU3yFlfo5oQCWSkbbzfdjDrAEjGc/edit?pli=1#slide=id.g27e787578a0_0_323
Wiki : https://square-piano-115.notion.site/NonaHackers-Wiki-1e7fb9b5c22f42d7a0cf94353222a595
References: NonaWorks BioSecurity Question Extance, A. (2015, September 22). Oligonucleotide drugs step up. Oligonucleotide Drugs Step up | Feature | Chemistry World. https://www.chemistryworld.com/features/oligonucleotide-drugs-step-up/8968.article Golden Gate Cloning - Wikipedia. (2017, April 26). Golden Gate Cloning - Wikipedia. https://en.wikipedia.org/wiki/Golden_Gate_Cloning Gibson Assembly - Snapgene. (n.d.). Gibson Assembly - Snapgene. https://www.snapgene.com/guides/gibson-assembly