Molecular mimicry of the NF-kappaB DNA target site by a selected RNA aptamer

Abstract

During the past two decades, structural and biophysical studies of DNA-protein and RNA-protein complexes have enhanced our understanding of the physico-chemical basis of nucleic acid recognition by proteins. However, it remains unclear what protein surface features are most important for nucleic acid binding and whether the same protein surface could bind specifically to both DNA and RNA. The recently described X-ray crystal structure of the transcription factor NF-kappaB p50 homodimer bound to a high-affinity RNA aptamer allows the direct comparison of NF-kappaB-RNA and NF-kappaB-DNA binding modes. The RNA aptamer, which bears no sequence homology to natural NF-kappaB DNA targets, adopts a structure with similar physico-chemical properties to kappaB DNA and contacts a common nucleic-acid-binding 'consensus surface' on the p50 homodimer.