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

SASDAT7 – Aptamer AIR-3 5FU

AIR3-5FU
MWexperimental 77 kDa
MWexpected 69 kDa
VPorod 77 nm3
log I(s) 1.82×104 1.82×103 1.82×102 1.82×101
AIR3-5FU small angle scattering data  s, nm-1
ln I(s)
AIR3-5FU Guinier plot ln 1.82×104 Rg: 4.3 nm 0 (4.3 nm)-2 s2
(sRg)2I(s)/I(0)
AIR3-5FU Kratky plot 1.104 0 √3 sRg
p(r)
AIR3-5FU pair distance distribution function Rg: 4.8 nm 0 Dmax: 16 nm

Data validation

Fits and models

log I(s)
 s, nm-1
AIR3-5FU DAMMIF model
Synchrotron SAXS data from solutions of Aptamer AIR-3 5FU 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 0.30 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.

AIR3-5FU
Mol. type   RNA
Olig. state   Dimer
Mon. MW   34.4 kDa
Sequence   FASTA