In vitro selection of RNA aptamers that bind the RNA-dependent RNA polymerase of hepatitis C virus: A possible role of GC-rich RNA motifs in NS5B binding

We employed SELEX (systematic evolution of ligands by exponential enrichment) and identified high affinity RNA aptamers to the hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp). GC-rich stretches were identified in many of the aptamers. Deletion of the 5′-end single-stranded GC-stretch (CGGG) of the highest binding RNA impaired the binding and the inhibitory activity of the RNA to NS5B RdRp. The majority of the mutants with a single base substitution on the CGGG motif exhibited weaker binding to NS5B. Interestingly, the CGGG motif is present on the stem structure of the NS5B coding RNA (5BSL3.2), which is considered to be an important cis-acting replication element. The 5BSL3.2 RNA showed substantial binding to NS5B, while a point mutation on the CGGG motif reduced the binding of RNA to NS5B. These results suggest a GC-stretch to be the RNA element recognized by NS5B.