Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-RasĀ and c-Kit promoter sequences.

Monsen RC, DeLeeuw LW, Dean WL, Gray RD, Chakravarthy S, Hopkins JB, Chaires JB, Trent JO, Nucleic Acids Res (2022) Europe PMC

SASDM46 – c-Kit12 DNase I Digest

c-Kit 12-tract G-quadruplex monomer Dnase I treated
MWexperimental 14 kDa
MWexpected 20 kDa
VPorod 16 nm3
log I(s) 2.07×10-1 2.07×10-2 2.07×10-3 2.07×10-4
c-Kit 12-tract G-quadruplex monomer Dnase I treated small angle scattering data  s, nm-1
ln I(s)
c-Kit 12-tract G-quadruplex monomer Dnase I treated Guinier plot ln 2.07×10-1 Rg: 1.6 nm 0 (1.6 nm)-2 s2
(sRg)2I(s)/I(0)
c-Kit 12-tract G-quadruplex monomer Dnase I treated Kratky plot 1.104 0 3 sRg
p(r)
c-Kit 12-tract G-quadruplex monomer Dnase I treated pair distance distribution function Rg: 1.6 nm 0 Dmax: 5.7 nm

Data validation


There are no models related to this curve.

Synchrotron SAXS data from solutions of c-Kit12 DNase I Digest in 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH 7.2 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory storage ring (Lemont, IL, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 3.5 m and at a wavelength of λ = 0.1033 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 230.00 μl sample at 1.4 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 25°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

C-Kit 12-tract G-quadruplex sequence digested by DNase I treatment prior to SEC-SAXS analysis.

c-Kit 12-tract G-quadruplex monomer Dnase I treated (c-Kit12 DnaseI treat)
Mol. type   DNA
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   20.4 kDa
Sequence   FASTA