FIGURE 4.

Mutations introduced into internal and terminal conserved elements for analyses of long-distance RNA–RNA interactions. (A) Positions within the PVX genome of conserved octanucleotide elements near the 5′ terminus (5′), upstream of the triple gene block (TB) and coat protein gene (CP). The conserved hexanucleotide element in the 3′ NTR (Hex) is also shown within an octanucleotide sequence that is also conserved. The 5′ and Hex elements are both complementary to the internal octanucleotide elements. Two other octanucleotide sequences (Pol and TB2) that are complementary to terminal elements are also illustrated. The position of the 850-nt template is shown above the CP gene as a horizontal arrow. (B) Mutations within the conserved elements are noted in red text. The top group of mutants was used to investigate minus-strand RNA synthesis both in vitro and in vivo because they could be tested in the context of both the 850-nt templates and in full-length transcripts. The lower group of mutants was only tested in vivo in the context of the full-length transcripts. (C) Predicted base pairs between the 5′ octanucleotide element or the hexanucleotide element (within the octanucleotide context) and internal elements.