14TSB_SynBio Automated Gene Assembly From Codons to Complete Genes and Pathways

Lead Research Organisation: Imperial College London
Department Name: Life Sciences

Abstract

The ability to assemble genes from smaller DNA fragments or generate combinatorial libraries of genetic mutations is fundamental to the field of synthetic biology. Different methodologies exist for their fabrication but enzymatic assembly produces consistently high quality products compared to other methods which is essential for downstream processes for improved characteristics (whether this is for improved strain phenotype or an improved protein function/yield). The potential to achieve this in a high throughput, automatable fashion would be a powerful and valuable tool for commercialisation in the synthetic biology arena. In this respect, we have previously developed a technology that can create random stretches of gene fragments using enzymatic additions of codon triplets. We now wish to investigate further procedures to assemble diversified gene fragments, in particular antibody variable loops, into whole genes in an automated fashion. Imperial College is automating assembly methods that would be enabling for the project by bridging the scale from codons to genes and pathways, thereby potentially the opening up new market areas.

Technical Summary

The ability to assemble genes from smaller DNA fragments or generate combinatorial libraries of genetic mutations is fundamental to the field of synthetic biology. Different methodologies exist for their fabrication but enzymatic assembly produces consistently high quality products compared to other methods which is essential for downstream processes for improved characteristics (whether this is for improved strain phenotype or an improved protein function/yield). The potential to achieve this in a high throughput, automatable fashion would be a powerful and valuable tool for commercialisation in the synthetic biology arena. In this respect, we have previously developed a technology that can create random stretches of gene fragments using enzymatic additions of codon triplets. We now wish to investigate further procedures to assemble diversified gene fragments, in particular antibody variable loops, into whole genes in an automated fashion. Imperial College is automating assembly methods that would be enabling for the project by bridging the scale from codons to genes and pathways, thereby potentially the opening up new market areas.

Planned Impact

The beneficiaries of this project can be defined as the researchers involved, and both the synthetic biology and academic communities as well as industry.
- Measurable impacts from this will include research output, interactions and presentations by the PI and PDRA at meetings both internally, externally and internationally, as well as the future placement of the PDRA involved.
The broader academic synthetic biology community will stand to benefit from this research.
- Measurable impacts from this research will be the development of new platform approaches that lead to the integration of codon diversification with DNA assembly of larger fragments.

Enzyme engineering is currently an enormous industry that underpins many biotech applications. The emergence of synthetic biology and its ability to more rapidly develop biological systems and new pathways for the production of fine chemicals in a sustainable manner will only increase the demand for new protein functionality and specificity. The technology that we present in this grant has the potential to be a disruptive technology in this space and radically alter the way that people perceive for evolving new functionality and specificity. Its application is not specific to a single domain but can be envisioned equally in antibody engineering for sensors, diagnostics and thereapeutics as well as enzymatic pathways for production of value chemicals.
- Measurable impacts will be implementation of the new platform within Isogenica and an ongoing collaboration between Imperial College and Isogenica.

The ethos of the Synthetic Biology community and CSynBI is to include public dialogue and outreach at every stage of research from tools to applications.
- Measurable impacts will be any future engagement activities undertaken during the lifetime of the grant.

Dissemination of results is a key feature of scientific research and the scientific endeavour.
- Measurable impacts will be publications and presentations during the lifetime of the grant and the following 12 months
 
Description We have further developed our DNA assembly technology
We have also discovered and characterised new DNA ligases that will improve the workflow of our industrial collaborator as well as improving our DNA assembly
Exploitation Route We aim to characterise the novel ligases further and commercially exploit them through licensing deals.
Sectors Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Our DNA technology has been used by Industry. We have the possibility of commercial exploitation of our findings
First Year Of Impact 2014
Sector Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description A semi-autonomous robot synthetic biologist for industrial biodesign and manufacturing
Amount £884,199 (GBP)
Funding ID EP/R034915/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2018 
End 08/2021
 
Description BBSRC Network in Biotechnology
Amount £99,000 (GBP)
Funding ID Sub project from University of Manchester who hold the main Network award 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2015 
End 05/2016
 
Description EPSRC Innovation and Knowledge Centre in Synthetic Biology - 24 month review
Amount £2,010,000 (GBP)
Funding ID (EP/N023854/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 12/2015 
End 11/2018
 
Description SynbiCITE - Innovation and Knowledge Centre in Synthetic Biology - Collaborative Programme - Tranche 1
Amount £2,907,115 (GBP)
Funding ID EP/M006700/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2014 
End 09/2017
 
Title BASIC DNA assembly 
Description This method provides for a highly scalable and efficient standardised method for assembling DNA parts to create new biological systems. 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact High throughput DNA assembly is currently being implemented on an automated workflow for industrial collaboration. We have collaborations with a number of academic and industrial partners to translate this technology. 
 
Description BioSynSys 2015 Biologie de synthese et des systemes 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The establishment of a French GDR for systems and synthetic biology is intended to bring together the collective efforts of the French nation in this area of research as well as providing a method for further international interaction. I was invited as a plenary speaker to their inaugural conference.
Year(s) Of Engagement Activity 2015
URL http://biosynsys2015.sciencesconf.org/?lang=en
 
Description Invited Seminar at University of Stuttgart 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a seminar to the Institut für Bioverfahrenstechnik
Year(s) Of Engagement Activity 2015
 
Description Invited seminar at LMU Munich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a plenary talk at the Institute retreat.
Year(s) Of Engagement Activity 2015
 
Description SynBioBeta London 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact SynBioBeta is a conference that acts as a hub at the academic and business interface of synthetic biology. The fast moving and adaptive field makes for a highly dynamic environment with the engagement of many SMEs and startups
Year(s) Of Engagement Activity 2015
URL http://synbiobeta.com/conferences/synbiobeta-london-2015/