Modification interference analysis of a self-cleaving RNA from hepatitis delta virus

A chemical modification-interference assay was used to evaluate the sequence requirements for self-cleavage of a 73-nucleotide self-cleaving RNA from the genomic hepatitis delta virus (HDV). Twenty-two nucleotides were categorized as individually essential for self-cleavage, shown by loss of activity when modified. All of these required nucleotides fell within 38 nucleotides downstream of the cleavage site, suggesting an essential structural or functional role for this region. Lesser effects were seen for nucleotides further 3' of the cleavage site, and a small number of nucleotides had a negligible effect on the extent of self-cleavage when modified. Several modifications increased the extent of self-cleavage, suggesting these nucleotides may act to inhibit the reaction when unmodified. The functional requirements for certain nucleotides are discussed in the light of structural probing data and conventional mutational analysis available for other HDV RNAs.