Biophysical characterization of the complex between the iron-responsive transcription factor Fep1 and DNA.

Miele AE, Cervoni L, Le Roy A, Cutone A, Musci G, Ebel C, Bonaccorsi di Patti MC, Eur Biophys J (2021) Europe PMC

SASDJ66 – GATA double strand DNA

24-mer double strand DNA from the GATA promoter
MWI(0) 10 kDa
MWexpected 14 kDa
VPorod 10 nm3
log I(s) 7.59×100 7.59×10-1 7.59×10-2 7.59×10-3
24-mer double strand DNA from the GATA promoter small angle scattering data  s, nm-1
ln I(s)
24-mer double strand DNA from the GATA promoter Guinier plot ln 7.59×100 Rg: 2.1 nm 0 (2.1 nm)-2 s2
(sRg)2I(s)/I(0)
24-mer double strand DNA from the GATA promoter Kratky plot 1.104 0 3 sRg
p(r)
24-mer double strand DNA from the GATA promoter pair distance distribution function Rg: 2.2 nm 0 Dmax: 7.4 nm

Data validation


Fits and models


log I(s)
 s, nm-1
24-mer double strand DNA from the GATA promoter PDB model

Synchrotron SAXS data from solutions of GATA double strand DNA in 50 mM MOPS, 50 mM NaCl, pH 7 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.09999 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 40.00 μl sample at 1.4 mg/ml was injected at a 0.40 ml/min flow rate onto a GE Superdex 75 Increase 5/150 column at 20°C. 900 successive 1 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.

The double strand portion of the GATA element has been exposed to X-ray beam at BM29 in Grenoble (ESRF, France) after having passed into a HPLC-SEC column. We have repeated the experiment in static dilution series and the results were reproducible. For consistency with the other samples, we decided to deposit only the SEC-SAXS data.

24-mer double strand DNA from the GATA promoter (GATAds)
Mol. type   DNA
Organism   synthetic oligonucleotide
Olig. state   Dimer
Mon. MW   6.8 kDa
Sequence   FASTA
 
PDB code   4I62