Structural Dynamics of Dengue Virus UTRs and Their Cyclization.

Robinson ZE, Pereira HS, D'Souza MH, Patel TR, Biophys J (2025) Europe PMC

SASDXT3 – Dengue Virus 2 (DENV2) RNA, 5' Untranslated region

DENV2 RNA, 5' Untranslated region
MWexperimental 44 kDa
MWexpected 57 kDa
VPorod 66 nm3
log I(s) 7.17×10-3 7.17×10-4 7.17×10-5 7.17×10-6
DENV2 RNA, 5' Untranslated region small angle scattering data  s, nm-1
ln I(s)
DENV2 RNA, 5' Untranslated region Guinier plot ln 7.18×10-3 Rg: 3.7 nm 0 (3.7 nm)-2 s2
(sRg)2I(s)/I(0)
DENV2 RNA, 5' Untranslated region Kratky plot 1.104 0 √3 sRg
p(r)
DENV2 RNA, 5' Untranslated region pair distance distribution function Rg: 3.8 nm 0 Dmax: 11.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
DENV2 RNA, 5' Untranslated region DAMMIN model
log I(s)
 s, nm-1
DENV2 RNA, 5' Untranslated region DAMMIN model
log I(s)
 s, nm-1
DENV2 RNA, 5' Untranslated region DAMMIN model
Synchrotron SAXS data from solutions of the 5' Untranslated region of DENV2 RNA in 10 mM Bis-Tris, 100 mM NaCl, 5 mM MgCl2, 15 mM KCl, 5% glycerol, pH 6 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 60.00 μl sample at 0.7 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW403-4F column at 25°C. 600 successive 3 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.

DENV2 RNA, 5' Untranslated region (DENV2 5' UTR)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   57.4 kDa
Sequence   FASTA