Selective binding of hepatitis C virus core protein to synthetic oligonucleotides corresponding to the 5' untranslated region of the viral genome.

Although it is assumed that hepatitis C virus (HCV) core protein binds with viral RNA to form a nucleocapsid, little is known about the resulting molecular interactions. We utilized surface plasmon resonance technology to study the structural basis of the affinity and the preference of the interaction between HCV core protein and oligonucleotides derived from the viral genome. Among the 10 oligonucleotides corresponding to the 5' untranslated region (5'UTR) of the tested HCV genome, the real-time analysis of sensorgrams indicated that the core protein binds most efficiently and stably to the 31-nucleotide-long sequence of the loop IIId domain, whose secondary structure is highly conserved not only among different HCV genotypes but also among pestiviruses. There also could be some interactions of the core protein with the loop I domain and the region of nt 23-41. The kinetic profiles, together with those obtained in experiments using single- and double-stranded polymeric oligonucleotides, suggest a multimerization of the core protein in solution. These newly characterized properties could provide a basis for understanding the pathway of the viral nucleocapsid assembly.