Saccharide–RNA recognition in a complex formed between neomycin B and an RNA aptamer

Abstract

The RNA aptamer complexes with tobramycin and neomycin B utilize common architectural principles to generate RNA-binding pockets for the bound aminoglycoside antibiotics. In each case, the 2-deoxystreptamine ring I and an attached pyranose ring are encapsulated within the major groove binding pocket, which is lined with mismatch pairs. The bound antibiotic within the pocket is capped over by a looped-out base and anchored in place through intermolecular hydrogen bonds involving charged amine groups of the antibiotic.

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

“…The NMR spectra of the neomycin-B-NEO1A complex matched well with the published spectra for the same complex (Jiang et al 1999), although some peaks were less intense and broader in our spectra (Fig. 2).…”

“…These less well-defined spectra are probably due to the difference in temperature of the previous (278K) and our (298K) NMR measurements. Nonetheless, the experimental and published spectra were similar enough to facilitate spectral assignments and to strongly indicate that the neomycin-B-NEO1A complex adopted the published structure (Jiang et al 1999). The secondary structure of NEO1A was predicted using RNAstructure4.6 (Mathews et al 2004).…”

“…The secondary structure of NEO1A was predicted using RNAstructure4.6 (Mathews et al 2004). For consistency with the previous NMR study, we adopted the numbering used in Jiang et al (1999) Table S2 for the buffers used to establish the effect of [I]. An adaptable pentaloop in the neomycin-B aptamer www.rnajournal.org 817…”

“…An NMR-derived structure is available for the NEO1A in complex with neomycin-B (Jiang et al 1999) but there is no equivalent structure for the apo-aptamer. To better understand the interaction of neomycin-B with NEO1A as it would occur inside cells where the aptamer might be applied in a regulatory role, we examined the aptamer-ligand interactions by a variety of means, including affinity measurements (isothermal titration calorimetry [ITC], and 2-aminopurine [2AP] steady state fluorescence), structural analysis (1D 1 H and 2D-NMR, 2AP fluorescence yield, analysis of sequence variants), and computational analysis by molecular docking.…”

The driving force for molecular evolution of translation

“…Here, a largely unstructured 11-base bulge loop and an opposed G fold into an elaborate three-dimensional cage that surrounds the ligand upon complex formation, incorporating the bound AMP into a GNRA tetraloop-like structure. Small-molecule ligand-induced RNA folding has also been observed in structural studies of several other aptamers, including those that bind vitamin B12 (Sussman et al 2000), theophylline (Zimmermann et al 1997), FMN (Fan et al 1996), and neomycin B (Jiang et al 1999b). …”