MoiRNAiFold: a novel tool for complex in silico RNA design

Area of Science:

• Computational Biology
• Synthetic Biology
• Molecular Biology

Background:

• Developing novel RNA constructs for diagnostics and therapeutics requires efficient in silico design tools.
• Current methods for synthetic RNA design are time-consuming and costly.
• There is a need for advanced software to handle complex RNA design constraints and improve regulatory functions.

Purpose of the Study:

• To introduce MoiRNAiFold, a user-friendly tool for de novo synthetic RNA design.
• To enhance the design of RNA molecules for gene expression regulation, including Translation Efficiency.
• To provide a powerful and accessible platform for complex RNA construct development.

Main Methods:

• MoiRNAiFold utilizes Constraint Programming with novel variable types, heuristics, and Large Neighborhood Search strategies.
• The software incorporates advanced features for RNA regulation, such as Translation Efficiency calculation.
• Benchmarking was performed using structural RNA puzzles from EteRNA and functional validation of designed riboregulators.

Main Results:

• MoiRNAiFold outperforms existing software in solving structural RNA puzzles.
• Designed RNA sequences, specifically riboregulators, demonstrate functionality in vitro and in vivo.
• The tool successfully handles numerous design constraints and quality measures for complex RNA constructs.

Conclusions:

• MoiRNAiFold is a powerful and versatile tool for de novo synthetic RNA design.
• The software significantly improves the design process for RNA constructs, particularly riboregulators.
• MoiRNAiFold is available as a free web server, facilitating advancements in RNA-based diagnostics and therapeutics.