Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

Kim D, Thiel B, Mrozowich T, Hennelly S, Hofacker I, Patel T, Sanbonmatsu K, Nature Communications 11(1) (2020) DOI

SASDHD3 – Braveheart in 6 mM MgCl2

Braveheart RNA
MWexperimental 205 kDa
MWexpected 205 kDa
VPorod 2380 nm3
log I(s) 2.20×10-1 2.20×10-2 2.20×10-3 2.20×10-4
Braveheart RNA small angle scattering data  s, nm-1
ln I(s)
Braveheart RNA Guinier plot ln 2.20×10-1 Rg: 11.8 nm 0 (11.8 nm)-2 s2
(sRg)2I(s)/I(0)
Braveheart RNA Kratky plot 1.104 0 √3 sRg
p(r)
Braveheart RNA pair distance distribution function Rg: 10.0 nm 0 Dmax: 28.7 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Braveheart RNA DAMMIN model
log I(s)
 s, nm-1
Braveheart RNA DAMMIN model
log I(s)
 s, nm-1
Braveheart RNA DAMMIN model
Synchrotron SAXS data from solutions of Braveheart in 6 mM MgCl2 in 50 mM HEPES-KOH, 100 mM KCl, 6 mM MgCl2, pH 7.6 were collected on the B21 beam line at the Diamond Light Source storage ring (Didcot, UK) using a Pilatus 2M detector at a sample-detector distance of 4 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 2 mg/ml was injected onto a column . 616 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.

The last 46 nucleotides are not part of Bvht. These were added as 3' structure cassette for primer extension after SHAPE and DMS probing. SEC-column type and SEC parameters (flow-rate, injection volume) = UNKNOWN; Experimental temperature = UNKNOWN.

Braveheart RNA (Bvht)
Mol. type   RNA
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   205.4 kDa
Sequence   FASTA