A sensitive RNA chaperone assay using induced RNA annealing by duplex specific nuclease for amplification

The hybridization of two complementary RNAs in single cells depends on their complementary sequences and secondary structures, and is usual inefficient at the low concentrations. The bacterial RNA chaperone Hfq increases the rate of base pairing hybridization of mRNA, and stabilizes sRNA-mRNA duplexes. However, The RNA chaperone Hfq accelerates the RNA annealing between two complementary pair RNAs with a still unknown mechanism. So the sensitivity assay of Hfq induced RNA annealing is very important. By using a 2-OMe-RNA modified molecular beacon as a reporter, which can be specificity cleavage by DSN, we observed the amplification reaction kinetics (κ_rea) is 0.16 s^-1. Our results showed that the Hfq hexamer directly induced the RNA annealing, and DSN aided the ultra-sensitivity assay reaction with 0.18 fM Hfq/RNA1/MB1.