Structural determinants of conformationally selective, prion-binding aptamers.
We have recently described the isolation of 2'-fluoropyrimidine-substituted RNA aptamers that bind selectively to disease-associated beta-sheet-rich forms of the prion protein, PrP, from a number of mammalian species. These aptamers inhibit the accumulation of protease-resistant forms of PrP in a prion-seeded, in vitro conversion assay. Here we identify the minimal portions of two of these aptamers that retain binding specificity. We determine their secondary structures by a combination of modeling and solution probing. Finally, we identify an internal site for biotinylation of a minimized, synthetic aptamer and use the resultant reagent in the detection of abnormal forms of PrP in vitro.
Sayer
Natalie M
NM
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom.
Cubin
Matthew
M
Rhie
Alexandre
A
Bullock
Marc
M
Tahiri-Alaoui
Abdessamad
A
James
William
W
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D019921:Biotinylation; D002417:Cattle; D004305:Dose-Response Relationship, Drug; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000378:metabolism; D007700:Kinetics; D008969:Molecular Sequence Data; D011328:Prions / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry; D014158:Transcription, Genetic; D014508:Urea / Q000494:pharmacology
D011328:Prions; D012313:RNA; D014508:Urea