Investigating RNA-RNA interactions through computational and biophysical analysis.

Mrozowich T, Park SM, Waldl M, Henrickson A, Tersteeg S, Nelson CR, De Klerk A, Demeler B, Hofacker IL, Wolfinger MT, Patel TR, Nucleic Acids Res (2023) Europe PMC

SASDQM9 – Japanese encephalitis virus 3' UTR RNA

Japanese encephalitis virus 3' UTR
MWexperimental 186 kDa
MWexpected 186 kDa
VPorod 2900 nm3
log I(s) 1.04×10-1 1.04×10-2 1.04×10-3 1.04×10-4
Japanese encephalitis virus 3' UTR small angle scattering data  s, nm-1
ln I(s)
Japanese encephalitis virus 3' UTR Guinier plot ln 1.04×10-1 Rg: 11.3 nm 0 (11.3 nm)-2 s2
(sRg)2I(s)/I(0)
Japanese encephalitis virus 3' UTR Kratky plot 1.104 0 √3 sRg
p(r)
Japanese encephalitis virus 3' UTR pair distance distribution function Rg: 11.2 nm 0 Dmax: 34.6 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Japanese encephalitis virus 3' UTR DAMMIN model
log I(s)
 s, nm-1
Japanese encephalitis virus 3' UTR DAMMIN model
log I(s)
 s, nm-1
Japanese encephalitis virus 3' UTR DAMMIN model
Synchrotron SAXS data from solutions of Japanese encephalitis virus 3' UTR RNA in 10 mM Bis-tris, 100 mM NaCl, 15 mM KCl 15 mM MgCl2, 10% glycerol, pH 5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A sample at 1.1 mg/ml was injected onto a Shodex 403KW-4F HPLC column at 15°C using a flow rate of 0.16 ml/min. Seven successive 3 second frames were collected through the SEC elution peak of the sample (from a total of 600 SEC-SAXS data frames). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Sample injection volume = UNKNOWN.

Japanese encephalitis virus 3' UTR (JEV 3' UTR)
Mol. type   RNA
Organism   Japanese encephalitis virus
Olig. state   Monomer
Mon. MW   185.7 kDa
Sequence   FASTA