• Research

Automated Nanoscale DNA Assembly

We are working to push the limits of the size and scale of DNA assembly and have recently automated the fabrication of large DNA assemblies in sub-microliter volumes at the Earlham Biofoundry.

The field of bioengineering is underpinned by our ability to assembly bespoke and complex DNA molecules at scale.  We are working to push the limits of the size and scale of DNA assembly and have recently automated the fabrication of large DNA assemblies in sub-microliter volumes at the Earlham Biofoundry. This has been coupled to validation using next-generation sequencing technologies.

Details.

The ease and costs of assembling DNA fragments can be reduced by standardizing the workflows allowing us to use automation to  increase throughput, improve reliability and decrease volumes.

The field of bioengineering is underpinned by our ability to reliably progress experimental workflows such as the assembly of DNA molecules at scale and the manipulation of genomic DNA. In 2015, we led the establishment of a common genetic syntax for the exchange of DNA parts for plants – the Phytobrick standard and have developed toolboxes of DNA parts as well as open source tools for the facile, iterative assembly of multigene constructs. 

These foundations have enabled us to break the limits of the size and scale of DNA assembly, automating the fabrication of large DNA assemblies in sub-microliter volumes in the Earlham Biofoundry. We have coupled this with automated workflows for bacterial transformation, colony picking and the purification of plasmid DNA, reducing the effort of the entire assembly workflow. 

Publications.

Phytobricks: Manual and Automated Assembly of Constructs for Engineering Plants.

Cai YM, Carrasco Lopez JA, Patron NJ. Methods Mol Biol. 2020;2205:179-199.

DOI: 10.1007/978-1-0716-0908-8_11. PMID: 32809200.

Systematic Tools for Reprogramming Plant Gene Expression in a Simple Model, Marchantia polymorpha. 

Sauret-Güeto S, Frangedakis E, Silvestri L, Rebmann M, Tomaselli M, Markel K, Delmans M, West A, Patron NJ, Haseloff J. 

ACS Synth Biol. 2020 Apr 17;9(4):864-882.

DOI: 10.1021/acssynbio.9b00511. Epub 2020 Apr 2. PMID: 32163700.

DNA assembly standards: Setting the low-level programming code for plant biotechnology.

Vazquez-Vilar M, Orzaez D, Patron N, In press, Plant Science (2018)

DOI: 10.1016/j.plantsci.2018.02.0243

Loop Assembly: a simple and open system for recursive fabrication of DNA circuits

Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F*, Haseloff J*, bioRxiv preprint (2018)

DOI: 10.1101/247593

SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms

D’Amore R, Johnson J, Haldenby S, Hall N, Hughes M, Joynson R, Kenny JG Patron NJ, Hertz-Fowler C and Hall A*, Biotechniques 63 (2017)

DOI: 10.2144/000114565

Blueprints for green biotech: development and application of standards for plant synthetic biology

Patron, N.J., Biochemical Society Transactions 44, 702-708 (2016)

DOI: 10.1042/BST20160044

Collaborators.

The OpenPlant Consortium

OpenPlant is a collaborative initiative between the University of Cambridge, the John Innes Centre and the Sainsbury Laboratory in Norwich. The initiative promotes interdisciplinary exchange, open technologies for innovation and responsible innovation for sustainable agriculture and conservation. The Development and application of standards for plant synthetic biology was a collaborative aim of the consortium to underpin the efforts in all work-packages.

The Liverpool GeneMill

GeneMill specializes in the fabrication of synthetic DNA providing end-to-end support from the design stage through to building sequence verified constructs.

Impact statement.

Synthetic biology applies engineering principles such as standardisation and modularisation to biological sciences through application of iterative design-build-test-learn cycles. The standardisation of biological components and reactions allows workflows to be automated. This provides the potential to revolutionise the speed and scale of research, increasing accuracy and allowing miniaturisation to reduce costs. The adoption of these principles and approaches enables scientists to pursue complex experimental designs.

Related reading.