SAXS/SANS on a model DIS heterocomplex

Aldrex Munsayac.

SASDUV8 – HIV-1 ²H-DIS-C:¹H-DIS-Gk RNA heterocomplex (DIS-Gk contrast matched in 65% v/v D₂O - SANS data)

HIV-1 dimerization initiation site with a CCCCCC apical loop
HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension
MWexperimental 5 kDa
MWexpected 30 kDa
log I(s) 2.07×10-2 2.07×10-3 2.07×10-4 2.07×10-5
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension small angle scattering data  s, nm-1
ln I(s)
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension Guinier plot ln 2.08×10-2 Rg: 1.6 nm 0 (1.6 nm)-2 s2
(sRg)2I(s)/I(0)
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension Kratky plot 1.104 0 √3 sRg
p(r)
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension pair distance distribution function Rg: 1.6 nm 0 Dmax: 5.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
HIV-1 dimerization initiation site with a CCCCCC apical loop HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension RNAMASONRY model
SANS data from solutions of the HIV-1 ²H-DIS-C:¹H-DIS-Gk RNA heterocomplex in 50 mM potassium phosphate buffer, 1 mM MgCl2, 50 mM NaCl, 65% v/v D2O, pH 7.5 were collected on the CG-3 bio-SANS instrument at the High Flux Isotope Reactor, Oak Ridge National Laboratory, (TN, USA) using a 2–dimensional linear position-sensitive detector detector at a sample-detector distance of 7 m and at a wavelength of λ = 0.6 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.20 mg/ml was measured at 20°C over a period of 37800 seconds. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

HIV-1 dimerization initiation site with a CCCCCC apical loop (DIS-C)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   9.3 kDa
Sequence   FASTA
 
HIV-1 DIS with a GGGGGG apical loop, UCU bulge, and 16 bp helical extension (DIS-Gk)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   20.8 kDa
Sequence   FASTA