Unraveling Prion Protein Interactions with Aptamers and Other PrP-Binding Nucleic Acids

Abstract

Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrPC) into the pathogenic conformer (PrPSc) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrPC to PrPSc. Several in vitro studies have described physical interactions between PrP and different classes of molecules, which might play a role in either PrP physiology or pathology. Among these molecules, nucleic acids (NAs) are highlighted as potential PrP molecular partners. In this context, the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) methodology has proven extremely valuable to investigate PrP–NA interactions, due to its ability to select small nucleic acids, also termed aptamers, that bind PrP with high affinity and specificity. Aptamers are single-stranded DNA or RNA oligonucleotides that can be folded into a wide range of structures (from harpins to G-quadruplexes). They are selected from a nucleic acid pool containing a large number (1014–1016) of random sequences of the same size (~20–100 bases). Aptamers stand out because of their potential ability to bind with different affinities to distinct conformations of the same protein target. Therefore, the identification of high-affinity and selective PrP ligands may aid the development of new therapies and diagnostic tools for TSEs. This review will focus on the selection of aptamers targeted against either full-length or truncated forms of PrP, discussing the implications that result from interactions of PrP with NAs, and their potential advances in the studies of prions. We will also provide a critical evaluation, assuming the advantages and drawbacks of the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technique in the general field of amyloidogenic proteins.

Liquid-liquid phase separation and aggregation of the prion protein globular domain modulated by a high-affinity DNA aptamer

“…PrP can interact with both DNA and RNA molecules and such interactions were described to occur in vitro and in vivo (14,16). Different binding affinities and stoichiometries were observed for PrP:NA complexes, depending on the NA size and sequence and on the PrP construct (17,18). Moreover, the effect of NA binding on the structure, oligomerization profile and toxicity of the resultant PrP species to mammalian cells in culture are also variable (19)(20)(21).…”

“…Other studies have further explored the NA binding ability of PrP to select and characterize NA sequences capable of binding to PrP C or the scrapie form with high affinity and specificity (17,(26)(27)(28), being valuable for therapeutic or diagnostic approaches. These sequences, named aptamers, were mostly identified by SELEX (Systematic Evolution of Ligands by Exponential Enrichment) (17).…”

“…Other studies have further explored the NA binding ability of PrP to select and characterize NA sequences capable of binding to PrP C or the scrapie form with high affinity and specificity (17,(26)(27)(28), being valuable for therapeutic or diagnostic approaches. These sequences, named aptamers, were mostly identified by SELEX (Systematic Evolution of Ligands by Exponential Enrichment) (17). Some of the identified NA aptamers significantly reduced PrP Sc formation in cell-free assays; aptamers that tightly bind to and stabilize PrP C are expected to block conversion and, thereby, prevent prion diseases (17,26,27,29).…”

“…These sequences, named aptamers, were mostly identified by SELEX (Systematic Evolution of Ligands by Exponential Enrichment) (17). Some of the identified NA aptamers significantly reduced PrP Sc formation in cell-free assays; aptamers that tightly bind to and stabilize PrP C are expected to block conversion and, thereby, prevent prion diseases (17,26,27,29). Other aptameric sequences were described to bind -sheet-enriched PrP structures, i.e.…”

“…Other aptameric sequences were described to bind -sheet-enriched PrP structures, i.e. scrapie-like forms, with application in the diagnostic of TSEs (17).…”