Molecular Recognition of Amino Acids by RNA-Aptamers: An L-Citrulline Binding RNA Motif and Its Evolution into an L-Arginine Binder

A pool of ∼10 15 different RNA molecules was enriched by in vitro selection for specific binding to L-citrulline [L-(+)-2-amino-5-ureidovaleric acid] in solution. Cloning and sequencing of the binding pool revealed two highly conserved regions present in all of the selected RNAs. These consensus sequences are 10 and 6 bases in length and are part of a defined secondary structure. All of the sequenced RNAs had the potential to fold into the same binding motif. On the basis of this motif, a 44 nucleotide long RNA was constructed. The dissociation constant of the 44-mer RNA and L-citrulline was determined by equilibrium gel filtration and by analytical column chromatography and was found to be 62-68 μM