Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor.

Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV, ACS Chem Biol 13(5):1235-1242 (2018) Europe PMC

SASDCF5 – Light encoded DNA biosensor: e13B DNA

e13B
MWI(0) 13 kDa
MWexpected 10 kDa
VPorod 13 nm3
log I(s) 1.75×101 1.75×100 1.75×10-1 1.75×10-2
e13B small angle scattering data  s, nm-1
ln I(s)
e13B Guinier plot ln 1.75×101 Rg: 1.8 nm 0 (1.8 nm)-2 s2
(sRg)2I(s)/I(0)
e13B Kratky plot 1.104 0 √3 sRg
p(r)
e13B pair distance distribution function Rg: 1.9 nm 0 Dmax: 7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
e13B DAMFILT model
Synchrotron SAXS data from solutions of Light encoded DNA biosensor: e13B DNA in 154 mM NaCl, pH 8.3 were collected at the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2 mg/ml were measured at 5°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 and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve. The model depicts the averaged spatial representation of the DNA (DAMFILT occupancy and volume-corrected bead model).

e13B
Mol. type   DNA
Olig. state   Monomer
Mon. MW   10.4 kDa
Sequence   FASTA