Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering.

Werner A, Konarev PV, Svergun DI, Hahn U, Anal Biochem 389(1):52-62 (2009) PubMed

SASDA54 – RNA Aptamer

MWexperimental 35 kDa
MWexpected 33 kDa
VPorod 38 nm3
log I(s) 2.25×102 2.25×101 2.25×100 2.25×10-1
SRB2m small angle scattering data  s, nm-1
ln I(s)
SRB2m Guinier plot ln 2.25×102 Rg: 2.8 nm 0 (2.8 nm)-2 s2
SRB2m Kratky plot 1.104 0 3 sRg
SRB2m pair distance distribution function Rg: 2.8 nm 0 Dmax: 10 nm

Experimental data validation

Fits and models

log I(s)
 s, nm-1
SRB2m DAMMIN model
Synchrotron SAXS data from solutions of RNA Aptamer in Hepes, pH 7.4 were collected on the EMBL X33 camera at the DORIS III storage ring (Hamburg, Germany) using a MAR 345 Image Plate detector (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). at 15°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

SRB2m (SRB2m)
Mol. type   RNA
Olig. state   Dimer
Mon. MW   16.6 kDa
Sequence   FASTA