The limits of specificity: An experimental analysis with RNA aptamers to MS2 coat protein variants

It has been hypothesized that selections for aptamers with high affinity fo r a given target molecule will of necessity identify aptamers that have hig h specificity for that target. We have attempted to assess this hypothesis by selecting aptamers that can bind to MS2 coat protein or to single- or do uble-substitution variants of the coat protein. Some aptamers selected to b ind MS2 coat protein or its variants were mildly specific for their cognate targets, discriminating by two- to fourfold against closely related protei ns. Specificity determinants on both the coat proteins and the aptamers cou ld be identified. However, many aptamers could readily bind to each of the different coat proteins. The identification of such aptamer 'generalists' b elies the proposed relationship between the affinities and specificities of selected RNA ligands. These results imply that, while aptamers may not fin ely discriminate between closely related targets, neither will their bindin g be negated by mutations in targets. Aptamer pharmaceuticals may therefore better resist the evolution of resistance.