Ribomaker

Ribomaker designs bacterial riboregulation systems by computationally optimizing small regulatory RNAs (sRNAs) and 5'-untranslated regions (5' UTRs) to control gene expression.

Key Features:

• Automated design: Reads sequence and structure specifications and optimizes sequences for sRNAs and 5' UTRs to promote desired intermolecular interactions.
• Evolutionary design strategy: Introduces random mutations and selects variants using a physicochemical model that evaluates free energy calculations to identify optimal regulatory sequences.
• Sequence–function prediction: Predicts sequence-function relationships to guide design of RNA molecules with specified regulatory behaviors.
• Experimental validation compatibility: Outputs sequences that can be directly tested in laboratory experiments to validate riboregulatory function.

Scientific Applications:

• Design of gene expression control systems: Generate optimized sRNA and 5' UTR sequences for custom bacterial gene expression regulation in synthetic biology.
• Genetic circuit construction: Support construction and optimization of synthetic genetic circuits that employ riboregulation.
• Study of riboregulation mechanisms: Provide computational predictions and designed variants to investigate RNA-mediated gene regulation in natural systems.

Methodology:

Reads sequence and structure specifications; optimizes sRNA and 5' UTR sequences; applies an evolutionary strategy introducing random mutations; evaluates variants using a physicochemical model with free energy calculations; and predicts sequence-function relationships and intermolecular interactions.