An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures.

ABSTRACT: Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP) fluorescence studies of the aptamer identified a flexible pentaloop and a sta

SUBMITTER: Ilgu M 

PROVIDER: S-EPMC4024636 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature