basicsynbio and the BASIC SEVA collection: software and vectors for an established DNA assembly method

Matthew C Haines; Benedict Carling; James Marshall; Vasily A Shenshin; Geoff S Baldwin; Paul Freemont; Marko Storch

doi:10.1093/synbio/ysac023

basicsynbio and the BASIC SEVA collection: software and vectors for an established DNA assembly method

Synth Biol (Oxf). 2022 Oct 11;7(1):ysac023. doi: 10.1093/synbio/ysac023. eCollection 2022.

Authors

Matthew C Haines^{1

2}, Benedict Carling³, James Marshall³, Vasily A Shenshin⁴, Geoff S Baldwin^{4

5}, Paul Freemont^{1

2

6}, Marko Storch^{1

2}

Affiliations

¹ Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.
² London Biofoundry, Imperial College Translation and Innovation Hub, London W12 0BZ, UK.
³ Department of Bioengineering, Imperial College London, London, Westminster SW7 2AZ, UK.
⁴ Department of Life Sciences, Imperial College London, London, Westminster SW7 2AZ, UK.
⁵ Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.
⁶ UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.

Abstract

Standardized deoxyribonucleic acid (DNA) assembly methods utilizing modular components provide a powerful framework to explore designs and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use and enables hierarchical assemblies through an idempotent format. These features enable applications including pathway engineering, ribosome binding site (RBS) tuning, fusion protein engineering and multiplexed guide ribonucleic acid (RNA) expression. In this work, we present basicsynbio, open-source software encompassing a Web App (https://basicsynbio.web.app/) and Python Package (https://github.com/LondonBiofoundry/basicsynbio), enabling BASIC construct design via simple drag-and-drop operations or programmatically. With basicsynbio, users can access commonly used BASIC parts and linkers while designing new parts and assemblies with exception handling for common errors. Users can export sequence data and create instructions for manual or acoustic liquid-handling platforms. Instruction generation relies on the BasicBuild Open Standard, which is parsed for bespoke workflows and is serializable in JavaScript Object Notation for transfer and storage. We demonstrate basicsynbio, assembling 30 vectors using sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA vector collection is compatible with BASIC and Golden Gate using BsaI. Vectors contain one of six antibiotic resistance markers and five origins of replication from different compatibility groups. The collection is available via Addgene under an OpenMTA agreement. Furthermore, vector sequences are available from within the basicsynbio application programming interface with other collections of parts and linkers, providing a powerful environment for designing assemblies for bioengineering applications. Graphical Abstract.

Keywords: DNA assembly; bioinformatics; cloning; synthetic biology; vectors.