Evolutionary design and analysis of ribozyme-based logic gates

A main goal of synthetic biology is the design of logic gates that can reprogram cells to perform various user-defined tasks. One approach is the use of ribozyme-based logic gates (ribogates) consisting of catalytic RNA strands. However, existing ribogate design approaches face limitations in terms...

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Bibliographic Details
Published in:Genetic programming and evolvable machines 2023-12, Vol.24 (2), Article 11
Main Authors: Kamel, Nicolas, Kharma, Nawwaf, Perreault, Jonathan
Format: Article
Language:English
Subjects:
Artificial Intelligence
Biological evolution
Biology
Biomedical Engineering and Bioengineering
Boolean functions
Compilers
Complexity
Computer Science
Design analysis
Electrical Engineering
Evolutionary algorithms
Gates
Interpreters
Logic circuits
Programming Languages
Programming Techniques
Software Engineering/Programming and Operating Systems
Synthetic biology
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Summary:A main goal of synthetic biology is the design of logic gates that can reprogram cells to perform various user-defined tasks. One approach is the use of ribozyme-based logic gates (ribogates) consisting of catalytic RNA strands. However, existing ribogate design approaches face limitations in terms of complexity, diversity, ease of use, and reliability. To address these challenges, we introduce a multi-objective evolutionary algorithm called Truth-Seq-Er, which generates diverse and complex ribogate designs while improving user-friendliness and accessibility. Truth-Seq-Er uses a quality diversity approach and a novel technique called viability nullification to design 1, 2, and 3-input integrated ribogates that implement both linearly separable and inseparable functions. By requiring only a target Boolean function as input, the algorithm eliminates the need for domain knowledge and streamlines the design process. The diverse designs generated by Truth-Seq-Er are robust against unexpected requirements and provide a large, unbiased dataset for characterizing candidate ribogates. Moreover, we propose a graph-based model for ribogate operation and analyze the design principles shared by different ribogate families. The results demonstrate the potential of Truth-Seq-Er in advancing ribogate design and contributing to the development of novel synthetic biology and unconventional computing applications. Truth-Seq-Er is available for download at https://github.com/nickkamel/Truth_Seq_Er_CLI .
ISSN:1389-2576
1573-7632
DOI:10.1007/s10710-023-09459-x