Optimization of Structure‐Guided Development of Chemical Probes for the Pseudoknot RNA of the Frameshift Element in SARS‐CoV‐2

Ceylan B, Adam J, Toews S, Kaiser F, Dörr J, Scheppa D, Tants J, Smart A, Schoth J, Philipp S, Stirnal E, Ferner J, Richter C, Sreeramulu S, Caliskan N, Schlundt A, Weigand J, Göbel M, Wacker A, Schwalbe H, Angewandte Chemie International Edition (2025) DOI

SASDVZ3 – SARS-CoV2 RNA pseudoknot at 4 mg/mL

SARS-CoV2 RNA pseudoknot
MWexperimental 24 kDa
MWexpected 22 kDa
VPorod 29 nm3
log I(s) 5.50×10-2 5.50×10-3 5.50×10-4 5.50×10-5
SARS-CoV2 RNA pseudoknot small angle scattering data  s, nm-1
ln I(s)
SARS-CoV2 RNA pseudoknot Guinier plot ln 5.50×10-2 Rg: 2.3 nm 0 (2.3 nm)-2 s2
(sRg)2I(s)/I(0)
SARS-CoV2 RNA pseudoknot Kratky plot 1.104 0 √3 sRg
Dmax: 7.9 nm

Data validation

There are no models related to this curve.

Synchrotron SAXS data from solutions of SARS-CoV2 RNA pseudoknot in 25 mM potassium phosphate, 50 mM KCl, pH 6.2 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123982 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 4.00 mg/ml was measured at 20°C. 35 successive 0.095 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.

Note: Possible repulsive interparticle interference present in the sample.

SARS-CoV2 RNA pseudoknot (SARS-CoV2 PK)
Mol. type   RNA
Organism   Severe acute respiratory syndrome coronavirus 2
Olig. state   Monomer
Mon. MW   22.3 kDa
Sequence   FASTA