Table 1.

Binding characteristics of mammalian PrPs and nucleic acids.

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

We chose the KD (dissociation constant) value of the best interaction when several aptamers were described by the same study. When many types of PrP were investigated in binding assays, the PrP species or fragment with the lowest KD value is the first shown. NS: non-SELEX (NA sequences found individually); ND: non-determined.