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 (PROTEIN DATA BANK) 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 ID   4I62