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

Area of Science:

• Synthetic Biology
• Molecular Biology
• Bioengineering

Background:

• Standardized DNA assembly methods are crucial for efficient synthetic biology workflows.
• The Biopart Assembly Standard for Idempotent Cloning (BASIC) offers a modular, accurate, and automatable approach to DNA assembly.
• Existing tools may lack comprehensive features for designing and implementing BASIC constructs.

Purpose of the Study:

• To introduce basicsynbio, an open-source software for designing DNA constructs using the BASIC assembly standard.
• To provide a user-friendly platform for both programmatic and graphical design of BASIC assemblies.
• To facilitate the creation and automation of synthetic biology experiments.

Main Methods:

• Development of basicsynbio, including a Web App and Python Package.
• Implementation of drag-and-drop functionality and programmatic design options.
• Integration of exception handling for common design errors and generation of liquid-handling instructions based on the BasicBuild Open Standard.
• Demonstration using the Standard European Vector Architecture (SEVA) collection.

Main Results:

• basicsynbio enables easy design and assembly of BASIC DNA constructs.
• The software supports programmatic access to parts and linkers, including custom designs.
• Generated instructions are compatible with automated liquid-handling platforms.
• A collection of 30 BASIC SEVA vectors was assembled and made available via Addgene.

Conclusions:

• basicsynbio provides a powerful and accessible environment for designing DNA assemblies.
• The software streamlines the Design-Build-Test-Learn cycle in synthetic biology.
• It supports diverse bioengineering applications through standardized and modular DNA assembly.