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 2009 Jun 1;389(1):52-62 PubMed

SASDA54 – RNA Aptamer

SRB2m
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
(sRg)2I(s)/I(0)
SRB2m Kratky plot 1.104 0 3 sRg
p(r)
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 X33 camera on the storage ring DORIS III (Hamburg, Germany). Using a MAR 345 Image Plate detector (s = 4π sin θ/λ, where 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 and the different curves were scaled for protein concentration.

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