RNA triplex structures revealed by WAXS-driven MD simulations

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

SASDKR5 – RNA Short Tetraloop Hairpin Duplex in 5 mM MgCl2

RNA Short Tetraloop Hairpin Duplex
MWexperimental 13 kDa
MWexpected 13 kDa
log I(s) 2.77×101 2.77×100 2.77×10-1 2.77×10-2
RNA Short Tetraloop Hairpin Duplex small angle scattering data  s, nm-1
ln I(s)
RNA Short Tetraloop Hairpin Duplex Guinier plot ln 2.78×101 Rg: 2.1 nm 0 (2.1 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: 2.3 nm 0 Dmax: 7.8 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of RNA Short Tetraloop Hairpin Duplex in 5 mM MgCl2 in 5 mM MgCl2, 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 2.30 mg/ml was measured at 10°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