Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes.

Czech A, Konarev PV, Goebel I, Svergun DI, Wills PR, Ignatova Z, Sci Rep 9(1):2465 (2019) Europe PMC

SASDDP5 – Mutant mammalian prion protein mRNA (octo-repear PrP mRNA) with KCl and pyridostatin (PDS)

octo-repeat PrP mRNA mutant
MWI(0) 185 kDa
MWexpected 144 kDa
VPorod 260 nm3
log I(s) 1.27×105 1.27×104 1.27×103 1.27×102
octo-repeat PrP mRNA mutant small angle scattering data  s, nm-1
ln I(s)
octo-repeat PrP mRNA mutant Guinier plot ln 1.27×105 Rg: 9.2 nm 0 (9.2 nm)-2 s2
(sRg)2I(s)/I(0)
octo-repeat PrP mRNA mutant Kratky plot 1.104 0 √3 sRg
p(r)
octo-repeat PrP mRNA mutant pair distance distribution function Rg: 9.9 nm 0 Dmax: 33 nm

Data validation

Fits and models

log I(s)
 s, nm-1
octo-repeat PrP mRNA mutant DAMFILT model
Synchrotron SAXS data from solutions of mutant mammalian prion protein mRNA (octo-repear PrP mRNA) in 10 mM Tris buffer with 100 mM KCl and 1 mM PDS, pH 7.5 were collected on the EMBL-P12 beam line at the PETRA III storage ring (DESY, Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 4 mg/ml were measured at 20°C. 20 successive 0.050 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

octo-repeat PrP mRNA mutant (PrPmRNA_mut)
Mol. type   RNA
Organism   human PrP ORF
Olig. state   Dimer
Mon. MW   71.8 kDa
Sequence   FASTA