MASON

MASON designs peptide nucleic acids (PNAs) complementary to bacterial mRNA translational start sites and predicts potential off-target interactions to optimize antisense oligomer specificity.

Key Features:

• Targeted PNA Design: Generates peptide nucleic acids (PNAs) complementary to the translational start site of a specified bacterial gene.
• Off-Target Prediction: Predicts potential off-target interactions based on experimental data from Salmonella enterica serovar Typhimurium treated with PNAs carrying serial mismatches and reports possible unintended interactions.
• Experimental Data Integration: Incorporates growth inhibition and RNA-sequencing (RNA-seq) findings to inform and refine off-target predictions.
• Mismatch Effect Validation: Accounts for observations that PNAs with terminal mismatches can still target essential genes such as acpP, with corroborating studies in uropathogenic Escherichia coli (UPEC).

Scientific Applications:

• Antibacterial antisense oligomer design: Design sequence-specific PNAs aimed at inhibiting bacterial gene translation while minimizing off-target effects for RNA antibiotic development.
• Off-target assessment in gene inhibition studies: Evaluate and predict unintended interactions in bacterial transcriptomes using mismatch-derived and RNA-seq data.
• Pathogen-targeted therapeutic development: Enable design of PNAs targeting genes in pathogens such as Salmonella enterica serovar Typhimurium and uropathogenic Escherichia coli (UPEC).

Methodology:

Generates PNA sequences complementary to target bacterial mRNA translational start sites, assesses potential off-target interactions using experimental mismatched PNA datasets, and leverages growth inhibition and RNA-sequencing (RNA-seq) data to refine predictions.