TY - JOUR T1 - A Codon Constrained Method for Both Eliminating and Creating Intragenic Bacterial Promoters JF - bioRxiv DO - 10.1101/2021.08.04.454459 SP - 2021.08.04.454459 AU - Dominic Y. Logel AU - Ellina Trofimova AU - Paul R. Jaschke Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/08/04/2021.08.04.454459.abstract N2 - Future applications of synthetic biology will require refactored genetic sequences devoid of internal regulatory elements within coding sequences. These regulatory elements include cryptic and intragenic promoters which may constitute up to a third of predicted Escherichia coli promoters. Promoter activity is dependent on the structural interaction of core bases with a σ factor. Rational engineering can be used to alter key promoter element nucleotides interacting with σ factors and eliminate downstream transcriptional activity. In this paper, we present COdon Restrained Promoter SilEncing (CORPSE), a system for removing intragenic promoters. CORPSE exploits the DNA-σ factor structural relationship to disrupt σ70 promoters embedded within gene coding sequences, with a minimum of synonymous codon changes. Additionally, we present an inverted CORPSE system, iCORPSE, which can create highly active promoters within a gene sequence while not perturbing the function of the modified gene.Competing Interest StatementThe authors have declared no competing interest. ER -