Unravelling structural dynamics of Dengue virus 3' UTR and its impact on viral life cycle

Trushar Patel.

SASDS49 – Dumbbell RNA - 3' UTR of Dengue virus

Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus
MWexperimental 33 kDa
MWexpected 31 kDa
VPorod 44 nm3
log I(s) 1.72×10-2 1.72×10-3 1.72×10-4 1.72×10-5
Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus small angle scattering data  s, nm-1
ln I(s)
Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus Guinier plot ln 1.73×10-2 Rg: 3.6 nm 0 (3.6 nm)-2 s2
(sRg)2I(s)/I(0)
Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus Kratky plot 1.104 0 √3 sRg
p(r)
Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus pair distance distribution function Rg: 3.6 nm 0 Dmax: 11.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus DAMMIN model
log I(s)
 s, nm-1
Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus DAMMIN model
log I(s)
 s, nm-1
Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus DAMMIN model
Synchrotron SAXS data from solutions of dumbbell RNA - 3' UTR of Dengue virus - in 20 mM HEPES, 100 mM NaCl, 5 mM MgCl2, pH 7 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 40.00 μl sample at 1.5 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW403-4F column at 15°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.

Dumbbell RNA - 3' untranslated region (3' UTR) Dengue virus (Dumbbell - 3' UTR)
Mol. type   RNA
Organism   dengue virus type 2
Olig. state   Monomer
Mon. MW   31.3 kDa
Sequence   FASTA