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It has been proposed that the hepatitis C virus (HCV) internal ribosome entry site (IRES) resides within a locked conformation, owing to annealing of its immediate flanking sequences. In this study, structure probing using Escherichia coli dsRNA-specific RNase III and other classical tools showed that this region switches to an open conformation triggered… (More)

A generalized p-cycle is a digraph whose set of vertices can be partitioned into p parts that are cyclically ordered in such a way that the vertices in one part are adjacent only to vertices in the next part. Any digraph can be shown as a p-cycle with p = 1, and bipartite di-graphs are generalized p-cycles with p = 2. A maximally connected digraph is said… (More)

Hepatitis C virus (HCV) RNA is recognized and cleaved in vitro by RNase P enzyme near the AUG start codon. Because RNase P identifies transfer RNA (tRNA) precursors, it has been proposed that HCV RNA adopts structural similarities to tRNA. Here, we present experimental evidence of RNase P sensitivity conservation in natural RNA variant sequences, including… (More)

In this paper, a method for obtaining large diameter 6 graphs by replacing some vertices of a Moore bipartite diameter 6 graph with complete K h graphs is proposed. These complete graphs are joined to each other and to the remaining nonmodified graphs by means of new edges and by using a special diameter 2 graph. The degree of the graph so constructed… (More)

Here, we show that Escherichia coli Ribonuclease III cleaves specifically the RNA genome of hepatitis C virus (HCV) within the first 570 nt with similar efficiency within two sequences which are 400 bases apart in the linear HCV map. Demonstrations include determination of the specificity of the cleavage sites at positions C27 and U33 in the first (5')… (More)