Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site

Spectroscopic and calorimetric techniques have been employed to characterize the impact on an Escherichia coli rRNA A-site model oligonucleotide of incorporating the fluorescent base analog 2-aminopurine into the 1492- or the 1493-position, as well as the energetics and dynamics associated with recognition of this A-site model oligomer by aminoglycoside antibiotics. The results of these studies indicate that incorporation of 2AP into either the 1492- or the 1493-position does not perturb the structure or stability of the host RNA or its aminoglycoside binding affinity. In addition, the results also highlight drug-induced reduction in the mobilities of the bases at both the 1492- and 1493-positions as a potentially key determinant of bactericidal potency.