Open Dataset XSSOSU8C

Correlating the Structure and Gene Silencing Activity of Oligonucleotide-Loaded Lipid Nanoparticles Using Small-Angle X-Ray Scattering


Individual ASO-LNP samples and the screening sample plates were prepared by a robotic liquid handler-assisted, high-throughput solvent-injection method that we developed previously. Briefly, a liquid handler (TECAN EVO, NC, USA) was used to dispense the ASO dissolved in a citrate buffer (25 mM, pH 4) into a 96-well sample plate, as well as to mix individual lipid stocks at certain molar ratios to generate different lipid mixtures. Formulated ASO-LNPs composed of 40 mol% MC3, 2 mol% DMG-PEG-2k, 10 mol% DSPC, and 48 mol% cholesterol at an N/P ratio of 2 for SAXS features assignments. The LNPs in pre-purification conditions (1:3 volume ratio of ethanol : 25 mM citrate buffer, pH 4) exhibited sharp SAXS features, indicating highly-ordered LNP morphology. The 4 mM total lipid concentration showed two overlapping but distinguishable peaks at q = 0.126 Å-1 and 0.139 Å-1. Using the relationship d = 2π/q, where d is the distance between lipid/ASO/water repeated structures, the peaks show organized structures spaced at d = 50 Å and 45 Å, respectively. The maxima at d = 50 Å is associated with the hexagonal phase (HII). Confirming this assignment are the two apparent ancillary peaks at q = 0.218 Å-1 and 0.251 Å-1 that would be expected for hexagonal packing at a 50 Å distance. Although the main peak splitting between the 50 and 45 Å are less significant at lower (2 and 1 mM) total lipid concentrations.

Experimental description

SAXS data were collected in the high throughput mode (HT-SAXS) using the Advanced Light Source SIBYLS beamline 12.3.1 at the Lawrence Berkeley National Laboratory (CA, USA). X-ray wavelength was set at λ = 1.216 Å, and the sample-to-detector distance was 2070 mm, resulting in a scattering vector, q, ranging from 0.01 Å-1 to 0.45 Å-1. The scattering vector is defined as q = 4πsinθ/λ, where 2θ is the scattering angle. Experiments were performed at 20 °C as described elsewhere 29. Briefly, the sample was exposed for 10 s with the detector framing at 0.3 s to maximize the signal while merging the SAXS signal using the SAXS FrameSlice application ( No radiation damage was observed during the 10 s exposure, and all collected frames were merged.

File description

1mM_LNP.dat , 2mM_LNP.dat, 4mM_LNP.dat fi are final merged SAXS curve at 1,2 and 4 mM total lipid concentration





Data collection technique


Journal DOI




1.216 Å

Sample to Detector Distance

2.07 m

Submitting Author

Michal Hammel

Lawrence Berkeley National Laboratory, The SIBYLS Beamline

United States of America

[email protected]


Project Leader

Michal Hammel

[email protected]

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  • Macromolecule 1: ASO-LNP
    • Sample Full Name: ASO-LNP
    • Sample Type: Other
    • Source Organism:
    • Source Organism NCBI Taxonomy ID:
    • Expression System:
    • Expression NCBI Taxonomy ID:
    • Sequence or Chemical Formula: