Structure and target interaction of a G-quadruplex RNA-aptamer.

Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U, RNA Biol 13(10):973-987 (2016) Europe PMC

SASDAU7 – Aptamer AIR-3 FdU

AIR3-FdU
MWexperimental 67 kDa
MWexpected 69 kDa
VPorod 67 nm3
log I(s) 1.75×104 1.75×103 1.75×102 1.75×101
AIR3-FdU small angle scattering data  s, nm-1
ln I(s)
AIR3-FdU Guinier plot ln 1.75×104 Rg: 5 nm 0 (5 nm)-2 s2
(sRg)2I(s)/I(0)
AIR3-FdU Kratky plot 1.104 0 √3 sRg
p(r)
AIR3-FdU pair distance distribution function Rg: 5 nm 0 Dmax: 16 nm

Data validation

Fits and models

log I(s)
 s, nm-1
AIR3-FdU DAMMIF model
Synchrotron SAXS data from solutions of Aptamer AIR-3 FdU in water, pH 7.5 were collected on the EMBL P12 beam line at the PETRA III storage ring (DESY; Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.12 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.20 mg/ml was measured at 10°C. 20 successive 0.050 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.

AIR3-FdU
Mol. type   RNA
Olig. state   Dimer
Mon. MW   34.4 kDa
Sequence   FASTA