Fig. 2. UV cross-linking of wild-type and mutant promoter-proximal RNAs to a 40 kDa host protein. The le and tr RNA sequences are shown above in blocks of six nucleotides, which are shown schematically as boxes below. The first two boxes are always striped, as these two hexamers are conserved between le and tr RNA. The subsequent sequences are poorly conserved, and are shown as white boxes for le RNA, and black boxes for tr RNA. The le and tr RNAs and the various chimeric tr/le RNAs (le 1–18 to 1–48) are shown schematically next to the cross-linking gel. The various promoter-proximal RNAs were mixed with HeLa cell cytoplasmic extracts and irradiated with 312 nm light for 10 min [or kept in the dark as a control (not shown), Materials and methods]. The reactions were then digested with RNase A, and separated on 12.5% protein gels to determine the relative abilities of these small RNAs to cross-link to host proteins. The cytopathic nature (CPE) of rSeV expressing these chimeric tr/le sequences in the leader region of G/Pr (Garcin et al., 1998) is indicated on the left; NA, not applicable as these rSeV were not prepared.