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Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy.

Authors
  • Yang, Y
  • Kochoyan, M
  • Burgstaller, P
  • Westhof, E
  • Famulok, M
Type
Published Article
Journal
Science (New York, N.Y.)
Publication Date
May 31, 1996
Volume
272
Issue
5266
Pages
1343–1347
Identifiers
PMID: 8650546
Source
Medline
License
Unknown

Abstract

In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.

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