In vitro selection of RNA aptamers against HCV-NS3 helicase and their structural similarity with 3'(+)UTR of HCV.

In order to screen and study of RNA aptamers against HCV NS3 helicase domain, we performed in vitro selection using two kinds of RNA pools, N30H and N30V. After eight selection cycles, RNA aptamers obtained from N30H pool possessed 5' extended single-stranded regions and the conserved sequence [5'-GGA(U/C)GGAGCC-3'] at stem-loop regions. On the other hand RNA aptamers obtained from another pool, N30V, possessed 3' long single-stranded regions with several stem-loop structures. All these aptamers showed strong inhibition of helicase activity in vitro, especially #5 represented Kd = 20 nM and IC50 approximately 50 nM. Interestingly these RNA aptamers showed similar secondary structural configuration with positive-stranded 3' untranslated region [3'(+)UTR]. It is known that 3'UTR of HCV is important for replication of HCV and also has strong affinity with NS3 protein. We will discuss the interaction of NS3 and 3'(+)UTR.