Phosphorothioate cap analogs stabilize mRNA and increase translational efficiency in mammalian cells

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Abstract
Capped RNAs synthesized by in vitro transcription have found wide utility for studying mRNA function and metabolism and for producing proteins of interest. We characterize here a recently synthesized series of cap analogs with improved properties that contain a sulfur substitution for a nonbridging oxygen in either the α-, β-, or γ-phosphate moieties, m27,2′-OGpppSG, m27,2′-OGppSpG, and m27,2′-OGpSppG, respectively. The new compounds were also modified at the 2′-O position of the m7Guo to make them anti-reverse cap analogs (ARCAs), i.e., they are incorporated exclusively in the correct orientation during in vitro transcription. Each of the S-ARCAs exists in two diastereoisomeric forms (D1 and D2) that can be resolved by reverse-phase HPLC. A major in vivo pathway for mRNA degradation is initiated by removal of the cap by the pyrophosphatase Dcp1/Dcp2, which cleaves between the α- and β-phosphates. Oligonucleotides capped with m27,2′-OGppSpG (D2) were completely resistant to hydrolysis by recombinant human Dcp2 in vitro, whereas those capped with m27,2′-OGppSpG (D1) and both isomers of m27,2′-OGpppSG were partially resistant. Luciferase mRNA capped with m27,2′-OGppSpG (D2) had a t1/2 of 257 min in cultured HC11 mammary epithelial cells compared with 86 min for m7Gp3G-capped mRNA. Luciferase mRNAs capped with m27,2′-OGppSpG (D1) and m27,2′-OGppSpG (D2) were translated 2.8-fold and 5.1-fold, respectively, more efficiently in HC11 cells than those capped with m7Gp3G. The greater yield of protein due to combining higher translational efficiency with longer t1/2 of mRNA should benefit applications that utilize RNA transfection such as protein production, anti-cancer immunization, and gene therapy.