RNA triplex structures revealed by WAXS-driven MD simulations

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

SASDKX5 – RNA Long Tetraloop Hairpin Duplex in 5 mM MgCl2

RNA Long Tetraloop Hairpin Duplex
MWexperimental 21 kDa
MWexpected 21 kDa
log I(s) 6.88×101 6.88×100 6.88×10-1 6.88×10-2
RNA Long Tetraloop Hairpin Duplex small angle scattering data  s, nm-1
ln I(s)
RNA Long Tetraloop Hairpin Duplex Guinier plot ln 6.88×101 Rg: 2.9 nm 0 (2.9 nm)-2 s2
(sRg)2I(s)/I(0)
RNA Long Tetraloop Hairpin Duplex Kratky plot 1.104 0 √3 sRg
p(r)
RNA Long Tetraloop Hairpin Duplex pair distance distribution function Rg: 2.9 nm 0 Dmax: 10.3 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of RNA Long 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 3.10 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 Long Tetraloop Hairpin Duplex (LT-DPX)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   20.6 kDa
Sequence   FASTA