Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM.

Monsen RC, Chua EYD, Hopkins JB, Chaires JB, Trent JO, Nucleic Acids Res (2023) Europe PMC

SASDPU6 – Duplex-G4-duplex DNA

Duplex-G4-duplex
MWexperimental 34 kDa
MWexpected 29 kDa
VPorod 59 nm3
log I(s) 4.10×100 4.10×10-1 4.10×10-2 4.10×10-3
Duplex-G4-duplex small angle scattering data  s, nm-1
ln I(s)
Duplex-G4-duplex Guinier plot ln 4.10×100 Rg: 3.2 nm 0 (3.2 nm)-2 s2
(sRg)2I(s)/I(0)
Duplex-G4-duplex Kratky plot 1.104 0 √3 sRg
p(r)
Duplex-G4-duplex pair distance distribution function Rg: 3.3 nm 0 Dmax: 13.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Duplex-G4-duplex AMBER model
Synchrotron SAXS data from solutions of duplex-G4-duplex DNA 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 (Lemont, IL, USA) using a Pilatus3 X 1M detector at a sample-detector distance of 3.6 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 240.00 μl sample at 6.6 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.

Sample is a synthetic duplex-G4-duplex DNA with a poly dT surrogate complement loop to facilitate G4 folding and maintenance.

Duplex-G4-duplex (DGD)
Mol. type   DNA
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   28.6 kDa
Sequence   FASTA