RNA triplex structures revealed by WAXS-driven MD simulations

Chen Y, He W, Kirmizialtin S, Pollack L, (2022) DOI

SASDKQ5 – RNA Short Tetraloop Hairpin Duplex in 200 mM KCl

RNA Short Tetraloop Hairpin Duplex
MWexperimental 13 kDa
MWexpected 13 kDa
log I(s) 1.96×101 1.96×100 1.96×10-1 1.96×10-2
RNA Short Tetraloop Hairpin Duplex small angle scattering data  s, nm-1
ln I(s)
RNA Short Tetraloop Hairpin Duplex Guinier plot ln 1.97×101 Rg: 2.0 nm 0 (2.0 nm)-2 s2
(sRg)2I(s)/I(0)
RNA Short Tetraloop Hairpin Duplex Kratky plot 1.104 0 √3 sRg
p(r)
RNA Short Tetraloop Hairpin Duplex pair distance distribution function Rg: 2.0 nm 0 Dmax: 6.8 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of RNA Short Tetraloop Hairpin Duplex in 200 mM KCl in 200 mM KCl, 20 mM Na-MES, 50 μM EDTA, pH 5.5 were collected on the 16-ID (LiX) beam line at the National Synchrotron Light Source II (NSLS-II) storage ring (Upton, NY, USA) using a Pilatus3 S 1M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.092 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.32 mg/ml was measured at 4°C. 15 successive 1 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.

RNA Short Tetraloop Hairpin Duplex (hpRNA)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   12.9 kDa
Sequence   FASTA