Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge.

Meier M, Moya-Torres A, Krahn NJ, McDougall MD, Orriss GL, McRae EKS, Booy EP, McEleney K, Patel TR, McKenna SA, Stetefeld J, Nucleic Acids Res 46(10):5319-5331 (2018) Europe PMC

SASDCC8 – Human TERC 1-20 DNA G-quadruplex

Human telomerase RNA template component, DNA counterpart, nucleotides 1-20
MWI(0) 14 kDa
MWexpected 13 kDa
VPorod 15 nm3
log I(s) 5.46×10-2 5.46×10-3 5.46×10-4 5.46×10-5
Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 small angle scattering data  s, nm-1
ln I(s)
Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 Guinier plot ln 5.47×10-2 Rg: 1.4 nm 0 (1.4 nm)-2 s2
(sRg)2I(s)/I(0)
Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 Kratky plot 1.104 0 √3 sRg
p(r)
Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 pair distance distribution function Rg: 1.4 nm 0 Dmax: 4.6 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 DAMMIN model
log I(s)
 s, nm-1
Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 DAMMIN model
log I(s)
 s, nm-1
Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 DAMMIN model
Synchrotron SEC-SAXS data collection was performed at the B21 beamline of the Diamond Light Source (UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). 50 µl purified hTERC 1-20 DNA G-quadruplex at a concentration of 5.58 mg/ml was injected into a 4.6 ml Shodex KW402.5-4F size exclusion column at a flow rate of 0.16 ml/min that was connected to the SAXS flow cell (25°C). The column diluted the sample 3-fold to approximately 2 mg/ml. Each frame was exposed for 3 seconds. 9 frames of the sample peak region were integrated, buffer subtracted and merged using the ScÅtter software package (http://www.bioisis.net/scatter). Guinier Rg, I(0) and their standard uncertainties were determined with GNOM/DATRG from ATSAS suite 2.8.2 (https://www.embl-hamburg.de/biosaxs/software.html). The Porod volume was calculated with DATPOROD from the ATSAS suite. The molecular weight derived from I(0) was calculated with SAXSMoW2 (http://saxs.ifsc.usp.br) and corrected for the appropriate mass density of the G-quadruplex DNA (1.85 g/cm³).

Human telomerase RNA template component, DNA counterpart, nucleotides 1-20 (TERC DNA)
Mol. type   DNA
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   6.4 kDa
Sequence   FASTA