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

SASDHC3 – Braveheart in 0 mM MgCl2

Braveheart RNA
MWexperimental 205 kDa
MWexpected 205 kDa
VPorod 2150 nm3
log I(s) 4.70×10-1 4.70×10-2 4.70×10-3 4.70×10-4
Braveheart RNA small angle scattering data  s, nm-1
ln I(s)
Braveheart RNA Guinier plot ln 4.70×10-1 Rg: 9.9 nm 0 (9.9 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: 9.8 nm 0 Dmax: 30 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 0 mM MgCl2 in 50 mM HEPES-KOH, 100 mM KCl, 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 1.9 mg/ml was injected onto a column . 620 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 in the sequence 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