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) Europe PMC

SASDA84 – RNA Aptamer

SRB2m
MWexperimental 20 kDa
MWexpected 33 kDa
VPorod 24 nm3
log I(s) 1.80×102 1.80×101 1.80×100 1.80×10-1
SRB2m small angle scattering data  s, nm-1
ln I(s)
SRB2m Guinier plot ln 1.80×102 Rg: 2.3 nm 0 (2.3 nm)-2 s2
(sRg)2I(s)/I(0)
SRB2m Kratky plot 1.104 0 √3 sRg
p(r)
SRB2m pair distance distribution function Rg: 2.3 nm 0 Dmax: 8 nm

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 beam line at the DORIS III, DESY storage ring (Hamburg, Germany) using a MAR 345 Image Plate detector (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.50 mg/ml was measured at 15°C. Two successive 120 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.

Wavelength = UNKNOWN. Sample detector distance = UNKNOWN

Tags: X33
SRB2m (SRB2m)
Mol. type   RNA
Olig. state   Dimer
Mon. MW   16.6 kDa
Sequence   FASTA