Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.

Publication Type:

Journal Article

Source:

Chemistry & biology, Volume 15, Issue 10, p.1125-37 (2008)

Keywords:

2008, Aptamers, Nucleotide, Base Sequence, Basic Sciences Division, Binding Sites, Center-Authored Paper, Crystallography, X-Ray, Genomics Core Facility, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Proteomics Core Facility, Scientific Imaging Core Facility, Shared Resources, Substrate Specificity, Tetracycline, Water

Abstract:

The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.