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

SASDDG5 – Mammalian prion protein mRNA (PrP mRNA wild type)

octo-repeat PrP mRNA
MWI(0) 130 kDa
MWexpected 144 kDa
VPorod 165 nm3
log I(s) 2.47×104 2.47×103 2.47×102 2.47×101
octo-repeat PrP mRNA small angle scattering data  s, nm-1
ln I(s)
octo-repeat PrP mRNA Guinier plot ln 2.47×104 Rg: 7.4 nm 0 (7.4 nm)-2 s2
octo-repeat PrP mRNA Kratky plot 1.104 0 3 sRg
octo-repeat PrP mRNA pair distance distribution function Rg: 7.4 nm 0 Dmax: 25 nm

Data validation

Fits and models

log I(s)
 s, nm-1
octo-repeat PrP mRNA DAMFILT model

Synchrotron SAXS data from solutions of mammalian prion protein mRNA (PrP mRNA wild type) in 10 mM Tris buffer, 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 (PrPmRNA)
Mol. type   RNA
Organism   human PrP ORF
Olig. state   Dimer
Mon. MW   71.9 kDa
Sequence   FASTA