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

SASDDL5 – Mutant mammalian prion protein mRNA (octo-repeat PrP mRNA)

octo-repeat PrP mRNA mutant

MW^I(0)	130	kDa
MW^expected	144	kDa
V^Porod	150	nm³

log I(s) 2.54×10⁴ 2.54×10³ 2.54×10² 2.54×10¹

octo-repeat PrP mRNA mutant small angle scattering data

s, nm^-1

Log plot Log-Log plot

ln I(s)

octo-repeat PrP mRNA mutant Guinier plot

ln 2.55×10⁴ R_g: 7.0 nm 0 (7.0 nm)^-2 s²

(sR_g)²I(s)/I(0)

1.104 0 √3 sR_g

p(r)	R_g: 7.0 nm 0 D_max: 24 nm

Data validation

Experimental data range

p(r) fit to data

Metric

Value

s_min D_max / π

0.8

N_Shannon

Worse

Better

Metric

Value

p_cormap

χ²

0.100
1.112

Worse

Better

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

octo-repeat PrP mRNA mutant DAMFILT model

Synchrotron SAXS data from solutions of mutant mammalian prion protein mRNA (octo-repeat PrP mRNA) 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 mutant (PrPmRNA_mut)
Mol. type		RNA
Organism		human PrP ORF
Olig. state		Dimer
Mon. MW		71.8 kDa
Sequence		FASTA