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

SASDMK6 – cKit-8

cKit promoter 8-tract G-quadruplex
MWexperimental 14 kDa
MWexpected 12 kDa
VPorod 15 nm3
log I(s) 2.19×10-2 2.19×10-3 2.19×10-4 2.19×10-5
cKit promoter 8-tract G-quadruplex small angle scattering data  s, nm-1
ln I(s)
cKit promoter 8-tract G-quadruplex Guinier plot ln 2.20×10-2 Rg: 1.5 nm 0 (1.5 nm)-2 s2
(sRg)2I(s)/I(0)
cKit promoter 8-tract G-quadruplex Kratky plot 1.104 0 √3 sRg
p(r)
cKit promoter 8-tract G-quadruplex pair distance distribution function Rg: 1.5 nm 0 Dmax: 4.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
cKit promoter 8-tract G-quadruplex CHIMERA model
Synchrotron SAXS data from solutions of cKit-8 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 275.00 μl sample at 8.9 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 8-tract G-quadruplex (cKit-8)
Mol. type   DNA
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   12.2 kDa
Sequence   FASTA