Synthesis and biological validation of N7-(4-chlorophenoxyethyl) substituted dinucleotide cap analogs for mRNA translation

Abstract

Design, synthesis and biological validation of dinucleotide cap analogs, N7-(4-chlorophenoxyethyl)-G(5′)ppp(5′)G (5a) and N7-(4-chlorophenoxyethyl)-m3′-OG(5′)ppp(5′)G (5b) are reported. The effect of N7-(4-chlorophenoxyethyl) substitution on cap analogs has been evaluated with respect to its in vitro transcription by using T7 RNA polymerase capping efficiency, and translational activity. The gel shift assay indicates that the new cap analogs (5a, 5b) showed 77% and 76% capping efficiency respectively, whereas the standard cap analog, m7G(5′)ppp(5′)G has a capping efficiency of 63%. The capping efficiency experiment clearly demonstrates that the N7-modified analogs are good substrate for T7 RNA polymerase. It is noteworthy that the mRNA poly(A) capped with N7-(4-chlorophenoxyethyl)-m3′-OG(5′)ppp(5′)G (5b) was translated ∼1.64-fold more efficiently, while compound (5a) was translated ∼0.72-fold less efficiently than mRNA capped with standard cap analog. The observed low translation activity for (5a) could be due to stability in the form of dinucleotide cap analogs. Based on the substrate compatability of the N7 modification in dinucleotide form, these new analogs may be used for structure function studies as well as protein production.