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

SASDHB3 – Braveheart Fragment 3

Braveheart Fragment 3
MWexperimental 111 kDa
MWexpected 111 kDa
VPorod 492 nm3
log I(s) 1.20×10-1 1.20×10-2 1.20×10-3 1.20×10-4
Braveheart Fragment 3 small angle scattering data  s, nm-1
ln I(s)
Braveheart Fragment 3 Guinier plot ln 1.20×10-1 Rg: 6.5 nm 0 (6.5 nm)-2 s2
(sRg)2I(s)/I(0)
Braveheart Fragment 3 Kratky plot 1.104 0 √3 sRg
p(r)
Braveheart Fragment 3 pair distance distribution function Rg: 6.4 nm 0 Dmax: 20.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Braveheart Fragment 3 DAMMIN model
log I(s)
 s, nm-1
Braveheart Fragment 3 DAMMIN model
log I(s)
 s, nm-1
Braveheart Fragment 3 DAMMIN model
Synchrotron SAXS data from solutions of Braveheart Fragment 3 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 0.5 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.

This fragment contains nucleotides 291 to 588 of Braveheart RNA and 3' structure cassette for primer extension after SHAPE and DMS probing (nt # 589-634). SEC-column type and SEC parameters (flow-rate, injection volume) = UNKNOWN; Experimental temperature = UNKNOWN

Braveheart Fragment 3 (Bvht F3)
Mol. type   RNA
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   110.8 kDa
Sequence   FASTA