DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.

ABSTRACT: The binding of RNA molecules to proteins or other ligands can require extensive RNA folding to create an induced fit. Understanding the generality of this principle involves comparing structures of RNA before and after complex formation. Here we report the NMR solution structure of a 29-nt RNA aptamer whose crystal structure had previously been determined in complex with its transcription factor target, the p50(2) form of NF-kappaB. The RNA aptamer internal loop structure has pre-organized features that are also found in the complex, including non-canonical base pairing and cross-strand base stacking. Remarkably, the free RNA aptamer structure possesses a major groove that more closely resembles B-form DNA than RNA. Upon protein binding, changes in RNA structure include the kinking of the

SUBMITTER: Reiter NJ 

PROVIDER: S-EPMC2275087 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature