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

Ichiro Hirao, Andrew D. Ellington
Department of Chemistry, ICMB A4800, University of Texas at Austin, Austin, TX 78712, U.S.A.

Marc Spingola, David Peabody
Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, U.S.A.

Abstract
It has been hypothesized that selections for aptamers with high affinity for a given target molecule will of necessity identify aptamers that have high 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 double-substitution variants of the coat protein. Some aptamers selected to bind MS2 coat protein or its variants were mildly specific for their cognate targets, discriminating by two- to fourfold against closely related proteins. Specificity determinants on both the coat proteins and the aptamers could be identified. However, many aptamers could readily bind to each of the different coat proteins. The identification of such aptamer ’generalists‘ belies the proposed relationship between the affinities and specificities of selected RNA ligands. These results imply that, while aptamers may not finely discriminate between closely related targets, neither will their binding be negated by mutations in targets. Aptamer pharmaceuticals may therefore better resist the evolution of resistance.

Keywords
aptamer, coat protein, in vitro selection, molecular recognition, MS2, SELEX