rna aptamers specifically interact with the prion protein prp we have isolated rna aptamers which are directed against the recombinant syrian golden hamster prion protein rprp23231 rprpc fused to glutathione stransferase gst the aptamers did not recognize the fusion partner gst or the fusion protein gstrprp90231 rprp2730 which lacks 67 amino acids from the prp n terminus the aptamerinteracting region of prpc was mapped to the nterminal amino acids 23 to 52 sequence analyses suggest that the rna aptamers may fold into gquartetcontaining structural elements replacement of the g residues in the g quartet scaffold with uridine residues destroyed binding to prp completely strongly suggesting that the g quartet motif is essential for prp recognition individual rna aptamers interact specifically with prion protein in brain homogenates from wildtype mice c57bl6 hamsters syrian golden and cattle as shown by supershifts obtained in the presence of antiprp antibodies no interaction was observed with brain homogenates from prp knockout mice prnp00 specificity of the aptamerprp interaction was further confirmed by binding assays with antisense aptamer rna or a mutant aptamer in which the guanosine residues in the g tetrad scaffold were replaced by uridine residues the aptamers did not recognize prp2730 in brain homogenates from scrapieinfected mice rna aptamers may provide a first milestone in the development of a diagnostic assay for the detection of transmissible spongiform encephalopathies