Localization of binding site for encephalomyocarditis virus RNA polymerase in the 3'-noncoding region of the viral RNA

Nucleic Acids Res. 1995 Feb 11;23(3):377-82. doi: 10.1093/nar/23.3.377.


We previously showed that encephalomyocarditis (EMC) virus RNA-dependent RNA polymerase (3Dpol) binds specifically to 3'-terminal segments of EMC virus RNA. This binding, which depends on both the 3'-noncoding region (3'-NCR) and 3'-poly (A) tail [together denoted 3'-NCR(A)], may be an important step in the initiation of virus replication. In this paper, the 3'-NCR and 3'-poly(A) were separately transcribed then mixed, but no complex with 3Dpol was obtained, showing that covalent attachment of the 3'-poly(A) to the 3'-NCR is essential for complex formation. Mutational and deletion analyses localized a critical determinant of 3Dpol binding to a U-rich sequence located 38-49 nucleotides upstream of the 3'-poly(A). Similar analyses led to the identification of a sequence of A residues between positions +10 and +15 of the 3'-poly(A) which are also critical for 3Dpol binding. As U-rich and A-rich regions are important for 3Dpol binding, a speculative model is proposed in which 3Dpol induces and stabilizes the base-pairing of the 3'-poly(A) with the adjacent U-rich sequence to form an unusual pseudoknot structure to which 3Dpol binds with high affinity.

MeSH terms

  • Base Sequence
  • Binding Sites
  • DNA-Directed RNA Polymerases / metabolism*
  • Encephalomyocarditis virus / enzymology*
  • Models, Genetic*
  • Molecular Sequence Data
  • Mutation / physiology
  • Nucleic Acid Conformation
  • Poly A / metabolism
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • Recombinant Proteins / isolation & purification


  • RNA, Messenger
  • RNA, Viral
  • Recombinant Proteins
  • Poly A
  • DNA-Directed RNA Polymerases