Four small RNA self‐cleaving domains, the hammerhead, hairpin, hepatitis delta virus and Neurospora VS ribozymes, have been identified previously in naturally occurring RNAs. The secondary structures of these ribozymes are reasonably well understood, but little is known about long‐range interactions that form the catalytically active tertiary conformations. Our previous work, which identified several secondary structure elements of the VS ribozyme, also showed that many additional bases were protected by magnesium‐dependent interactions, implying that several tertiary contacts remained to be identified. Here we have used site‐directed mutagenesis and chemical modification to characterize the first long‐range interaction identified in VS RNA. This interaction contains a 3 bp pseudoknot helix that is required for tertiary folding and self‐cleavage activity of the VS ribozyme.

The North Atlantic right whale, Eubalaena glacialis (Müller, 1776), is one of the world's most endangered large cetaceans. It is widely believed that Basque whalers caused the most dramatic decline of this species in the western North Atlantic during the early-16th and 17th centuries. Previous osteological analysis of 17 historic bones suggested that 50% of the Basque harvest consisted of right whales and 50% of bowhead whales, Balaena mysticetus L., 1758. This 50:50 ratio has been used to estimate pre-exploitation population size, which has subsequently formed the basis of recovery goals and plans for the North Atlantic right whale. Genetic analysis of 21 bones, 13 identified as right whales and 8 as bowhead whales through osteological examination, indicates that in fact only 1 bone was a right whale and 20 were bowhead whales. Additionally, preliminary microsatellite analyses of this specimen are not consistent with the hypothesis that whaling resulted in the low genetic variation found in this species today. These results differ from what would be expected based on any previous view of Basque whaling, and raise questions regarding the impact of Basque whaling on this species.

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A North Atlantic right whale ( Eubalaena glacialis ) genomic library was developed and screened with a (GATA) 8 probe to identify tetranucleotide microsatellite loci. Sixteen characterized loci were polymorphic in North Atlantic and/or South Atlantic ( Eubalaena australis ) right whales, 12 being polymorphic in E. glacialis , and 15 in E. australis . Fourteen of these were combined with 21 other previously identified loci for a suite of 35 loci which can be used to increase resolution of genetic analyses of these species. Multiplex reactions were developed for genotyping samples at these loci, providing a method that is rapid, reliable and cost-effective.

Several examples of inhibition of the function of a ribozyme or RNA‐protein complex have shown that certain antibiotics can interact specifically with RNA. There are, however, few examples of antibiotics that have a positive, rather than a negative, effect on the function of an RNA. We have found that micromolar concentrations of viomycin, a basic, cyclic peptide antibiotic of the tuberactinomycin group, enhance the cleavage of a ribozyme derived from Neurospora VS RNA. Viomycin decreases by an order of magnitude the concentration of magnesium required for cleavage. It also stimulates an otherwise insignificant transcleavage reaction by enhancing interactions between RNA molecules. The ability of viomycin to enhance some RNA‐mediated reactions but inhibit others, including translation and Group I intron splicing, demonstrates the potential for natural selection by small molecules during evolution in the ‘RNA world’ and may have broader implications with respect to ribozyme expression and activity in contemporary cells.