Probing the statistics of sequence-dependent DNA conformations in solution using SAXS

Heidar Koning.

SASDVA7 – The 60bp dsDNA oligo GAGE6_3

GAGE6_3
MWexperimental 34 kDa
MWexpected 37 kDa
VPorod 80 nm3
log I(s) 1.50×10-2 1.50×10-3 1.50×10-4 1.50×10-5
GAGE6_3 small angle scattering data  s, nm-1
ln I(s)
GAGE6_3 Guinier plot ln 1.51×10-2 Rg: 5.0 nm 0 (5.0 nm)-2 s2
(sRg)2I(s)/I(0)
GAGE6_3 Kratky plot 1.104 0 3 sRg
p(r)
GAGE6_3 pair distance distribution function Rg: 5.6 nm 0 Dmax: 21.4 nm

Data validation


There are no models related to this curve.

Synchrotron SAXS data from solutions of The 60bp dsDNA oligo GAGE6_3 in 150 mM KCl, 20 mM HEPES, 5% glycerol, 5 mM MgCl2, 1 mM DTT, pH 7.5 were collected on the SAXS/WAXS beam line at the Australian Synchrotron storage ring (Melbourne, Australia) using a Pilatus3 S 2M detector at a sample-detector distance of 2.4 m and at a wavelength of λ = 0.10781 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.01 mg/ml was measured at 25°C. 400 successive 1 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.

The 60bp dsDNA duplex GAGE6_3: 5-GCCTTCTGCAAAGAAGTCTTGCGCATCGCGCGTGAAGGCGCGCGCTAGCGCGCGGATGCT-3 This data was collected at the Australian Synchrotron by injecting 50 µL of sample at 81 µM in 150mM KCl, 20mM HEPES (pH 7.4), 5% glycerol, 5mM MgCl2, 1mM DTT. This data is part of the manuscript: Probing the statistics of sequence-dependent DNA conformations in solution using SAXS.

GAGE6_3 (GAGE6_3)
Mol. type   DNA
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   18.6 kDa
Sequence   FASTA