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