Synthesis of low immunogenicity RNA with high-temperature in vitro transcription

ABSTRACT The use of synthetic RNA for therapeutics requires that the in vitro synthesis process be robust and efficient. The technology used for the synthesis of these in vitro-transcribed mRNAs, predominantly using phage RNA polymerases (RNAPs), is well established. However, transcripts synthesized with RNAPs are known to display an immune-stimulatory activity in vivo, that is often undesirable. Previous studies have identified double-stranded RNA (dsRNA), a major by-product of the in vitro transcription (IVT) process, as a trigger of cellular immune responses. Here we describe the characterization of a high-temperature IVT process using thermostable T7 RNAPs to synthesize functional mRNAs that demonstrate reduced immunogenicity without the need for a post-synthesis purification step. We identify features that drive the production of two kinds of dsRNA by-products—one arising from 3’ extension of the run-off product and one formed by the production of antisense RNAs—and demonstrate that at a high temperature, T7 RNAP has reduced 3’-self extension of the run-off product. We show that template-encoded poly-A tailing does not affect 3’-self extension but reduces the formation of the antisense RNA by-products and that combining high-temperature IVT with template-encoded poly-A tailing prevents formation of both kinds of by-products.