A conserved viral RNA fold enables nuclease resistance across kingdoms of life.

Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL, Nucleic Acids Res 53(16) (2025) Europe PMC

SASDVW4 – ST9a RNA, WT (54 nucleotides in 1 mM MgCl2; monomer)

ST9 WT (54 nt RNA)
MWexperimental 16 kDa
MWexpected 17 kDa
VPorod 20 nm3
log I(s) 3.81×100 3.81×10-1 3.81×10-2 3.81×10-3
ST9 WT (54 nt RNA) small angle scattering data  s, nm-1
ln I(s)
ST9 WT (54 nt RNA) Guinier plot ln 3.81×100 Rg: 1.7 nm 0 (1.7 nm)-2 s2
(sRg)2I(s)/I(0)
ST9 WT (54 nt RNA) Kratky plot 1.104 0 √3 sRg
p(r)
ST9 WT (54 nt RNA) pair distance distribution function Rg: 1.8 nm 0 Dmax: 5.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
ST9 WT (54 nt RNA) PYMOL model
Synchrotron SAXS data from solutions of ST9 RNA WT, (54 nucleotides) in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 1 mM MgCl2 were collected on the 16-ID (LiX) beam line at the National Synchrotron Light Source II (NSLS-II; Upton, NY, USA) using a Pilatus3 S 1M detector at a sample-detector distance of 4.1 m and at a wavelength of λ = 0.082 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 95.00 μl sample at 3 mg/ml was injected at a 0.75 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 1200 successive 2 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.

ST9 WT (54 nt RNA)
Mol. type   RNA
Olig. state   Monomer
Mon. MW   17.5 kDa
Sequence   FASTA