An alarm system for biomedical construct design: a lesson from the unintended protein product of eGFP

Abstract

Plasmids are widely used for gene expression, yet their coding potential beyond the intended coding sequence (CDS) is often poorly characterized. Here, we explored putative hidden open reading frames (hidden ORFs) embedded within non-canonical reading frames of plasmid sequences through a computational workflow for their identification. Using enhanced green fluorescent protein (eGFP) as a target gene, we observed unexpectedly uninterrupted ORFs in both the +2 coding frame and the reverse frame. Immunoblotting detected stable expression of the +2 frame-derived protein, but not the reverse-frame ORF. Motivated by these observations, we developed a computational pipeline and analyzed 6,308 eGFP-containing plasmids, identifying putative hidden ORFs in approximately 6% of constructs. Approximately 94% of hidden ORFs occurred in the +2 frame, with the remainder occurring in the reverse frame. The same analytical pipeline, if utilized for plasmids beyond eGFP plasmids, can contribute to avoiding unintended outcomes, in applications such as gene replacement therapy.