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. For the PEG-lipid screening, LNPs were designed with the lipid composition with molar percent of MC3 : DSPC : cholesterol : PEG-lipids at 40 : 10 : (100 - X) : X, where X = 1, 3, or 5, a total lipid concentration of 1 mM, and a N/P ratio of 2. The prepared lipid mixtures were rapidly mixed with the ASO aqueous phase at a volume ratio of 1 : 3 (50 μL : 150 μL) in the sample plate using the robot, allowing for self-assembly of ASO-loaded LNPs, which were then characterized for particle structure by SAXS in the preparation buffer.In separate experiments, certain LNPs were processed through ultracentrifugation using an Amicon filter with the MWCO of 10 kD (Millipore, MA, USA) for purification and buffer exchange to PBS.

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 (https://bl1231.als.lbl.gov/ran). No radiation damage was observed during the 10 s exposure, and all collected frames were merged.

PEGx_y.dat is a final merged SAXS profile , where x is a #ID of specific PEG-lipid and y is the molar ratio of PEG-lipid. \#1 DMPE (C14:0)-PEG0.55k - #2 DMPE(C14:0)-PEG1k #3 DMPE(C14:0)-PEG2k - #4 DPPE(C16:0)-PEG1k #5 DPPE(C16:0)-PEG2k - #6 DSPE(C18:0)-PEG0.55k #8 DSPE(C18:0)-PEG1k #9 DSPE(C18:0)-PEG2k - #10 DSPE(C18:0)-2arm-PEG2k- #11 DOPE(C18:1)-PEG0.55k #12 DOPE(C18:1)-PEG1k - #13 DOPE(C18:1)-PEG2k #14 DMG(C14:0)-PEG2k - #15 DSG(C18:0)-PEG2k #16 Ceramide(C8)-PEG0.75k #17 Ceramide(C8)-PEG2k - #18 Ceramide(C16)-PEG0.75k - #19 Ceramide(C16)-PEG2k

2023-02-07

2023-02-08

HT-SAXS

1.216 Å

2.07 m

Sample:

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