Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats.

D'Souza MH, Mrozowich T, Badmalia MD, Geeraert M, Frederickson A, Henrickson A, Demeler B, Wolfinger MT, Patel TR, Nucleic Acids Res 50(10):5881-5898 (2022) Europe PMC

SASDNL2 – LincRNA-p21 Sense Alu Inverted Repeat

LincRNA-p21 AluSx1 Sense RNA
MWexperimental 100 kDa
MWexpected 100 kDa
VPorod 225 nm3
log I(s) 1.00×10-2 1.00×10-3 1.00×10-4 1.00×10-5
LincRNA-p21 AluSx1 Sense RNA small angle scattering data  s, nm-1
ln I(s)
LincRNA-p21 AluSx1 Sense RNA Guinier plot ln 1.01×10-2 Rg: 6.1 nm 0 (6.1 nm)-2 s2
(sRg)2I(s)/I(0)
LincRNA-p21 AluSx1 Sense RNA Kratky plot 1.104 0 √3 sRg
p(r)
LincRNA-p21 AluSx1 Sense RNA pair distance distribution function Rg: 6.2 nm 0 Dmax: 18.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
LincRNA-p21 AluSx1 Sense RNA DAMMIN model
log I(s)
 s, nm-1
LincRNA-p21 AluSx1 Sense RNA DAMMIN model
log I(s)
 s, nm-1
LincRNA-p21 AluSx1 Sense RNA DAMMIN model
Synchrotron SAXS data from solutions of LincRNA-p21 sense Alu inverted repeat in 50mM HEPES,150 mM NaCl, 15 mM MgCl2, 3% glycerol, pH 7.4 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Pilatus 2M detector at a wavelength of λ = 0.154 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 2.5 mg/ml was injected onto a column . 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 parameters: UNKNOWN. Sample temperature: UNKNOWN.

LincRNA-p21 AluSx1 Sense RNA (AluSx1 Sense)
Mol. type   RNA
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   99.5 kDa
Sequence   FASTA