Mapping and characterization of G‐quadruplexes in monkeypox genomes

Pereira H, Gemmill D, Siddiqui M, Vasudeva G, Patel T, Journal of Medical Virology 95(5) (2023) DOI

SASDQK6 – Monkeypox viral synthetic DNA fragment (DNA sequence 2, MP2)

Monekypox DNA sequence 1
MWexperimental 6 kDa
MWexpected 6 kDa
VPorod 11 nm3
log I(s) 3.06×10-3 3.06×10-4 3.06×10-5 3.06×10-6
Monekypox DNA sequence 1 small angle scattering data  s, nm-1
ln I(s)
Monekypox DNA sequence 1 Guinier plot ln 3.06×10-3 Rg: 1.6 nm 0 (1.6 nm)-2 s2
(sRg)2I(s)/I(0)
Monekypox DNA sequence 1 Kratky plot 1.104 0 √3 sRg
p(r)
Monekypox DNA sequence 1 pair distance distribution function Rg: 1.6 nm 0 Dmax: 4.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Monekypox DNA sequence 1 DAMMIN model
log I(s)
 s, nm-1
Monekypox DNA sequence 1 DAMMIN model
log I(s)
 s, nm-1
Monekypox DNA sequence 1 DAMMIN model
Synchrotron SAXS data from solutions of Monkeypox viral synthetic DNA fragment (MP2) in 20 mM HEPES, 100 mM KCl, and 0.2 mM EDTA, pH 7.4 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 3.7 m and at a wavelength of λ = 0.094 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 40.00 μl sample at 1.0 mg/ml was injected onto a column at 15°C. 600 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.

SEC-column: UNKNOWN: SEC flow-rate: UNKNOWN.

Monekypox DNA sequence 1 (MP2)
Mol. type   DNA
Organism   Monkeypox virus
Olig. state   Monomer
Mon. MW   6.4 kDa
Sequence   FASTA