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

SASDAV7 – Aptamer AIR-3A

AIR-3A
MWexperimental 14 kDa
MWexpected 13 kDa
VPorod 14 nm3
log I(s) 1.69×103 1.69×102 1.69×101 1.69×100
AIR-3A small angle scattering data  s, nm-1
ln I(s)
AIR-3A Guinier plot ln 1.69×103 Rg: 1.9 nm 0 (1.9 nm)-2 s2
(sRg)2I(s)/I(0)
AIR-3A Kratky plot 1.104 0 √3 sRg
p(r)
AIR-3A pair distance distribution function Rg: 1.9 nm 0 Dmax: 6.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
AIR-3A DAMMIN model
log I(s)
 s, nm-1
AIR-3A SASREF model
Synchrotron SAXS data from solutions of Aptamer AIR-3A 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 0.40 mg/ml was measured at 10°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Number of frames = UNKNOWN

AIR-3A
Mol. type   RNA
Olig. state   Dimer
Mon. MW   6.4 kDa
Sequence   FASTA