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

SASDDK5 – Mammalian prion protein mRNA (PrP mRNA wild type) with KCl and pyridostatin (PDS)

octo-repeat PrP mRNA

MW^I(0)	170	kDa
MW^expected	144	kDa
V^Porod	220	nm³

log I(s) 1.26×10⁵ 1.26×10⁴ 1.26×10³ 1.26×10²

octo-repeat PrP mRNA small angle scattering data

s, nm^-1

Log plot Log-Log plot

ln I(s)

ln 1.27×10⁵ R_g: 9.1 nm 0 (9.1 nm)^-2 s²

(sR_g)²I(s)/I(0)

1.104 0 √3 sR_g

p(r)	R_g: 9.3 nm 0 D_max: 31 nm

Data validation

Experimental data range

p(r) fit to data

Metric

Value

s_min D_max / π

1.1

N_Shannon

Worse

Better

Metric

Value

p_cormap

χ²

0.320
0.845

Worse

Better

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

Synchrotron SAXS data from solutions of Mammalian prion protein mRNA (PrP mRNA wild type) 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 (PrPmRNA)
Mol. type		RNA
Organism		human PrP ORF
Olig. state		Dimer
Mon. MW		71.9 kDa
Sequence		FASTA