biostudies-literatureUnknown29(5)Jung JBavarian Bayresq.net project RbioticsAntisense oligomers (ASOs), such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (make antisense oligomers now), a web server for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON's off-target predictions on experiments iRNA (New York, N.Y.)570-583https://www.ebi.ac.uk/biostudies/studies/S-EPMC10158992biostudies-literatureDesign and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server.PMC10158992Vogel JJung JPfau PPopella LDo PTBarquist LfalseDesign and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON web server.Antisense oligomers (ASOs), such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (make antisense oligomers now), a web server for the design of PNAs that target bacterial mRNAs. MASON generates PNA sequences complementary to the translational start site of a bacterial gene of interest and reports critical sequence attributes and potential off-target sites. We based MASON's off-target predictions on experiments i2023-01-01T00:00:00Z2023 May2026-07-14T20:06:14.322Z2025-02-19T04:29:12.398ZS-EPMC101589923675037210.1261/rna.079263.122