Diving into the structural architecture of the B2 SINE ribozyme

Trushar Patel.

SASDV83 – B2 SINE ribozyme with deletion mutation 96-105

B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105
MWexperimental 65 kDa
MWexpected 54 kDa
VPorod 135 nm3
log I(s) 6.82×10-2 6.82×10-3 6.82×10-4 6.82×10-5
B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 small angle scattering data  s, nm-1
ln I(s)
B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 Guinier plot ln 6.82×10-2 Rg: 5.5 nm 0 (5.5 nm)-2 s2
(sRg)2I(s)/I(0)
B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 Kratky plot 1.104 0 √3 sRg
p(r)
B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 pair distance distribution function Rg: 5.7 nm 0 Dmax: 17.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 DAMMIN model
log I(s)
 s, nm-1
B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 DAMMIN model
log I(s)
 s, nm-1
B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 DAMMIN model
Synchrotron SAXS data from solutions of B2del96-105 RNA in 5 mM Tris-HCl, 10 mM NaCl, 0.01% NP-40, 0.02 mM EDTA, 0.2 mM DTT, 0.5 mM MgCl2 and 1.5 % Glycerol, pH 7.9 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 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 1.5 mg/ml was injected onto a Shodex 403KW-4F HPLC column at 15°C using a flow rate of 0.16 ml/min. 600 successive 3 second frames were collected. Eight successive 3 second frames were collected through the SEC elution peak of the sample. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

B2 short interspaced nuclear element (SINE) RNA with deletion mutation 96-105 (B2 del96-105)
Mol. type   RNA
Organism   Mus musculus
Olig. state   Monomer
Mon. MW   54.0 kDa
Sequence   FASTA