In vitro selection of ATP-binding receptors using a ribonucleopeptide complex

A recently described three-dimensional structure of the ribosome provides a sense of remarkable diversity of RNA-protein complexes, We have designed a new class of scaffold for artificial receptors, in which a short peptide and RNA with a randomized nucleotide region form a stable and specific complex. The randomized nucleotide region was placed next to the HIV-1 Rev response element to enable the formation of ribonucleopeptide pools in the presence of the Rev peptide. In vitro selection of RNA oligonucleotides from the randomized pool afforded a ribonucleopeptide receptor specific for ATP. The ATP-binding ribonucleopeptide did not share the known consensus nucleotide sequence for ATP aptamers and completely lost its ATP-binding ability in the absence of the Rev peptide. The ATP-binding activity of the ribonucleopeptide was increased by a substitution of the N-terminal amino acid of the Rev peptide. These results demonstrate directly that the peptide is incorporated in the functional structure of RNA and suggest that amino acids outside the RNA-binding region of the peptide modulate the ATIP-binding of ribonucleopeptide. Our approach would provide an alternative strategy for the design of tailor-made ribonucleopeptide receptors and enzymes.