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

SASDMN6 – cKit-12

cKit promoter 12-tract G-quadruplex
MWexperimental 21 kDa
MWexpected 20 kDa
VPorod 26 nm3
log I(s) 2.31×10-2 2.31×10-3 2.31×10-4 2.31×10-5
cKit promoter 12-tract G-quadruplex small angle scattering data  s, nm-1
ln I(s)
cKit promoter 12-tract G-quadruplex Guinier plot ln 2.31×10-2 Rg: 2.5 nm 0 (2.5 nm)-2 s2
(sRg)2I(s)/I(0)
cKit promoter 12-tract G-quadruplex Kratky plot 1.104 0 √3 sRg
p(r)
cKit promoter 12-tract G-quadruplex pair distance distribution function Rg: 2.6 nm 0 Dmax: 9 nm

Data validation

Fits and models

log I(s)
 s, nm-1
cKit promoter 12-tract G-quadruplex CHIMERA model
Synchrotron SAXS data from solutions of cKit-12 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 340.00 μl sample at 4.3 mg/ml was injected at a 0.70 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 22°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Storage temperature = UNKNOWN. Number of frames = UNKNOWN

cKit promoter 12-tract G-quadruplex (cKit-12)
Mol. type   DNA
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   20.4 kDa
Sequence   FASTA