7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system.

Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D, Nucleic Acids Res (2023) Europe PMC

SASDQ69 – 28 base pair DNA substrate (used in experiments with 7-deazapurine in DNA proteins)

Custom 28 base pair double stranded DNA
MWexperimental 22 kDa
MWexpected 17 kDa
VPorod 24 nm3
log I(s) 6.50×100 6.50×10-1 6.50×10-2 6.50×10-3
Custom 28 base pair double stranded DNA small angle scattering data  s, nm-1
ln I(s)
Custom 28 base pair double stranded DNA Guinier plot ln 6.50×100 Rg: 2.6 nm 0 (2.6 nm)-2 s2
(sRg)2I(s)/I(0)
Custom 28 base pair double stranded DNA Kratky plot 1.104 0 √3 sRg
p(r)
Custom 28 base pair double stranded DNA pair distance distribution function Rg: 2.8 nm 0 Dmax: 10.2 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Custom 28 base pair double stranded DNA GROMACS model
Synchrotron SAXS data from solutions of 28 base pair DNA in 100 mM KCl, 50 mM Tris pH 7.0, 1 mM DTT, pH 7 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1 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 sample at 1 mg/ml was injected at a 0.50 ml/min flow rate onto a Shodex PROTEIN KW-802.5 size exclusion column (8.0 mm I.D. x 300 mm) at 24.9°C. Scattering images were collected with 3-s exposures per frame over the course of 40 minutes. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Sample injection volume = UNKNOWN

Custom 28 base pair double stranded DNA (28bp dsDNA)
Mol. type   DNA
Organism   Synthetic, purchased from IDT technologies
Olig. state   Monomer
Mon. MW   17.3 kDa
Sequence   FASTA