Unraveling Prion Protein Interactions with Aptamers and Other PrP-Binding Nucleic Acids
Abstract
:1. Introduction
2. PrP and Nucleic Acids Interactions
3. SELEX Technique and the Aptamer Discovery
4. Nucleic Acids Aptamers against PrP
5. Aptamers against Other Amyloidogenic Proteins
6. Conclusions and Perspectives
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Author, Year (Ref.) | Nucleic Acid Type | KD 1 (nM) | Binding Assay | PrP SELEX Target | PrPs Recognized | PrP Binding Region(s) |
---|---|---|---|---|---|---|
Weiss, 1997 [33] | RNA-aptamer | ND | Gel-shift of labeled aptamer | Hamster rPrP23−231 | Mouse, hamster, cow (PrP in brain homogenates) | (23–36) |
Nandi, 1997 [29,30,31] | Plasmid DNA | 250 | Fluorescent dye displacement | NS | Human rPrP106–126 and rPrP23–231 | ND |
Cordeiro, 2001 [21] | Short dsDNAs | 25 | Fluorescence polarization | NS | Murine rPrP23–231 | N-terminal and C-terminal domains |
Gabus, 2001 [76] | HIV-1 LTR DNA (1000 bp) | ND | Gel-shift assay | NS | Human rPrP23–231 or 23–144 | N-terminal |
Gabus, 2001 [37] | HIV-1 5’-leader RNA (415 nt) | ND | Gel shift assay | NS | Human rPrP23–231; Ovine rPrP25–234 | N-terminal |
Proske, 2002 [62] | RNA-aptamer | 100 | Filter-binding assay | Human PrP90−129 | Hamster, mouse or human rPrP | (90–129) |
Adler, 2003 [22] | Small, highly structured RNAs | 3.8 | Gel shift, filter-binding assay | NS | Human rPrP, PrP from brain homogenates of mouse, rat and hamster | N-terminal domain |
Rhie, 2003 [63] | RNA-aptamer | 16 | Homologous competition binding assay | SAF material from infected brain homogenates | Bovine rPrP in b-oligomeric or a-helical form, PK-untreated SAF, PK-treated SAF | N-terminal and SAF conformation-specific site in (110–230) |
Sayer, 2004 [77] | RNA-aptamer | 6.8 | Equilibrium binding | Bovine rPrP23−230 | Bovine rPrP | ND |
Sekiya, 2005 [78] | RNA-aptamer | ND | ND | Murine rPrP23−231 and murine SAF infected material | Murine rPrP23–231 and mouse SAF | (23–108) of Murine rPrP and mouse SAF |
Sekiya, 2006 [79] | RNA-aptamer | 5.6 | Filter-binding assay | Murine rPrP23–231 with competitive selection | Murine rPrP23–231, Bovine rPrP, Mouse PrP in brain homogenate | (23–108) and (23–88) |
Mercey, 2006 [35] | RNA-aptamer | 15 | Surface plasmon resonance, filter-binding assay | Ovine PrP23–231 with mutations associated with disease | Ovine rPrP(ARR, VRQ, AHQ, ARQ), Murine rPrP, Bovine rPrP | (25–34) and (101–110) |
Lima, 2006 [34] | Short dsDNAs | 90 | Fluorescence polarization and SAXS | NS | Murine rPrP23–231 | N-terminal and C-terminal |
Takemura, 2006 [65] | DNA-aptamer | 16 | End-point titration method in microplate, gel-shift, and dot-blot assays | Human rPrP23−231 | Murine rPrP23–231, PrP from brain homogenates of sheep, calves, pigs, deer, PK-untreated PrP from ScN2a cells | (23–89) |
Ogasawara, 2007 [80] | DNA-aptamer | 100 | Surface plasmon resonance, dot-blot, competitive selection and fluorescence measurements | Murine rPrP23−231 | Murine rPrP23–231 | ND |
Murakami, 2008 [71] | RNA-aptamer | 31 | Surface plasmon resonance | Bovine PrP23−231 | Bovine rPrP23–231 | (125–231) |
Bibby, 2008 [81] | DNA-aptamer | 18 | Saturation binding using PrP-coated Ni-NTA beads | Ni-NTA beads coated Murine PrP90−231 | Murine rPrP90–231, Ovine rPrP and Human rPrP90–231 | (90–230) |
Mashima, 2009 [69] | G4 RNA-aptamer | 8.5 | Northwestern blotting assay | Bovine PrP23−231 | Bovine PrPC | (25–34) and (110–118) |
G4 RNA-aptamer | 280 | Amyloidogenic bovine PrP-β | ND | |||
G4 DNA-aptamer | 85 | Bovine PrPC | (25–34) and (110–118) | |||
G4 DNA-aptamer | >280 | Amyloidogenic Bovine PrP-β | ND | |||
Wang, 2011 [82] | DNA-aptamer biosensor immobilized | 22 | Surface plasmon resonance | PrPSc from brain tissues of scrapie-infected animals with counter-selection with PrPC | Pathological isoforms of PrP from distinct species | ND |
Macedo, 2012 [24] | Small dsDNAs | ND | Fluorescence measurements | NS | murine rPrP23–231 and rPrP109–149 | N-terminal and C-terminal domains |
Cavaliere, 2013 [36] | G4 DNA-aptamer | 62 | Surface plasmon resonance and Isothermal Titration Calorimetry (ITC) | Ovine rPrP-23–231 | Ovine rPrP23–24 | 23-134 |
G4 RNA-aptamer | 75 | Ovine rPrP23–24 | ||||
G4 DNA-aptamer | 300 | Amyloidogenic Ovine PrP-β | ND | |||
G4 RNA-aptamer | 400 | Amyloidogenic Ovine PrP-β |
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Macedo, B.; Cordeiro, Y. Unraveling Prion Protein Interactions with Aptamers and Other PrP-Binding Nucleic Acids. Int. J. Mol. Sci. 2017, 18, 1023. https://doi.org/10.3390/ijms18051023
Macedo B, Cordeiro Y. Unraveling Prion Protein Interactions with Aptamers and Other PrP-Binding Nucleic Acids. International Journal of Molecular Sciences. 2017; 18(5):1023. https://doi.org/10.3390/ijms18051023
Chicago/Turabian StyleMacedo, Bruno, and Yraima Cordeiro. 2017. "Unraveling Prion Protein Interactions with Aptamers and Other PrP-Binding Nucleic Acids" International Journal of Molecular Sciences 18, no. 5: 1023. https://doi.org/10.3390/ijms18051023