Identification of RNA ligands that bind hepatitis C virus polymerase selectively and inhibit its RNA synthesis from the natural viral RNA templates

Nam Viet Vo, Jong Won Oh, Michael M.C. Lai

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46 Citations (Scopus)


To identify the potential RNA inhibitors of HCV polymerase, we have isolated high-affinity RNA ligands specific to hepatitis C virus (HCV) NS5B protein from a combinatorial RNA library using the Systematic Evolution of Ligands by EXponential enrichment (SELEX) procedure. Thirty-seven selected ligands were classified into eight groups on the basis of their sequence homologies. Most (60%) of the ligands carry the conserved YGUAGR hexamer (Y = pyrimidine, R = purine) at the 5′ end of the 40-nt randomized region, and 74% of the ligands end in (A/C)U at the 3′end. However, strong binding to NS5B required the whole RNA ligand including the flanking conserved nucleotides at both ends. The binding of the selected ligands to NS5B is highly specific and strong, as reflected in their low dissociation rate constants (kd ∼ 10-4 s-1). Analysis of secondary structure by computer program and RNase footprints of the two different aptamers from two most conserved groups revealed RNA structures containing three stem loops with internal bulges. NS5B bound these RNA at a region between the two stem loops from the 5′ -end. Some of these RNA aptamers could serve as a template for the HCV polymerase, but some interfered with the activity of the viral enzyme. These RNA ligands will be useful for further characterization of NS5B-binding properties and, with further modifications, may have potential therapeutic value.

Original languageEnglish
Pages (from-to)301-316
Number of pages16
Issue number2
Publication statusPublished - 2003 Mar 15

Bibliographical note

Funding Information:
We thank Drs. Michael Chamberlin and Caroline Kane, and Kate Carroll and Linda D’Ari of University of California, Berkeley for helpful suggestions and some technical assistance, and Dr. Lilian Hsu of Mt. Holyoke College for critically reading the manuscript. This work was partially supported by an NIH Grant AI 47348. M.M.C.L. is an Investigator of the Howard Hughes Medical Institute.

All Science Journal Classification (ASJC) codes

  • Virology


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