Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome.

Watson JA, Pantier R, Jayachandran U, Chhatbar K, Alexander-Howden B, Kruusvee V, Prendecki M, Bird A, Cook AG, Life Sci Alliance 6(3) (2023) Europe PMC

SASDP74 – AT-rich DNA

AT-rich dsDNA
MWexperimental 7 kDa
MWexpected 7 kDa
VPorod 12 nm3
log I(s) 1.37×10-2 1.37×10-3 1.37×10-4 1.37×10-5
AT-rich dsDNA small angle scattering data  s, nm-1
ln I(s)
AT-rich dsDNA Guinier plot ln 1.37×10-2 Rg: 1.7 nm 0 (1.7 nm)-2 s2
(sRg)2I(s)/I(0)
AT-rich dsDNA Kratky plot 1.104 0 √3 sRg
p(r)
AT-rich dsDNA pair distance distribution function Rg: 1.6 nm 0 Dmax: 4.6 nm

Data validation

Fits and models

log I(s)
 s, nm-1
AT-rich dsDNA DAMMIN model
log I(s)
 s, nm-1
AT-rich dsDNA PYMOL model
Synchrotron SAXS data from solutions of AT-rich DNA in 20 mM Tris-HCl, pH 7.5, 200 mM NaCl, were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 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 45.00 μl sample at 5 mg/ml was injected at a 0.10 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 22°C. 619 successive 3 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 ATSAS 3.0.5 suite of software was used for processing data (Manalastas-Cantos et al., 2021).

AT-rich dsDNA
Mol. type   DNA
Olig. state   Monomer
Mon. MW   7.4 kDa
Sequence   FASTA