Sample Prep for Viral RNA Capture with LASSO

Team Dynamic Matrices | 24 August 2026

Conventional RNA purification uses chemical force: chaotropic salts, phenol, high-stringency washes. It works because it does not care what it captures. Sequence-selective capture is different. LASSO's catcher strands hybridise to the viral sequence you designed them for, and the polymer network condenses around it. That selectivity is the advantage, and it means the sample has to arrive in a state where hybridisation can happen. Sample preparation is part of the assay, not a chore before it. Here is what matters.

Lysis: gentler than you are used to

Chaotropic lysis (guanidinium) denatures everything, including the structure you may want to keep and the buffer conditions the capture chemistry needs. For direct capture from a lysate, we use detergent-based lysis:

• Triton X-100 or NP-40 at 0.5 to 1 percent in a Tris or HEPES buffer at physiological salt, with an RNase inhibitor. This opens enveloped virions and cells without denaturing RNA structure.
• Avoid bead beating and sonication for enveloped viruses in liquid samples; they shear RNA and generate heat. Reserve mechanical disruption for tissue or for non-enveloped viruses with robust capsids, and keep it short and cold.
• For swabs in viral transport medium, a direct detergent lysis of the VTM is usually enough. For plasma, add proteinase K (see below). For wastewater, concentrate first.

If your downstream application is diagnostic detection only, lysis can be more aggressive; if it is RNA structure, RNA-protein interaction or full-length sequencing, keep it gentle.

RNase protection: the most common failure

Clinical and environmental samples are full of RNase. Steps we do not skip:

1. RNase-free plastics and water, and a decontaminated bench.
2. RNase inhibitor (recombinant, 1 U/µL) in the lysis buffer.
3. Stabilisation on collection for samples that will travel: a guanidinium-based transport medium or a commercial RNA stabiliser, then a buffer exchange before capture (see below).
4. Cold, fast. Process within an hour of lysis or freeze the lysate at minus 80 °C once.

A degraded target with no intact catcher-complementary region looks like a capture failure. Check integrity on a representative sample before blaming the chemistry.

Inhibitors and debris

• Spin. 2 minutes at 10,000 g removes particulates, mucus and cell debris that interfere with polymer condensation. Losing a little target in the pellet is worth the cleaner supernatant.
• Proteinase K for protein-rich samples (plasma, serum, sputum): 10 minutes at 56 °C, then 5 minutes at 95 °C to inactivate. This clears nucleoprotein complexes and RNases at once. Heat inactivation is short enough that RNA damage is minimal.
• Concentrate low-titre samples before capture. For wastewater, PEG precipitation or ultrafiltration; for large-volume culture supernatant, ultrafiltration. Capture kinetics depend on target concentration, so concentrating first improves recovery.

Buffer compatibility with the capture chemistry

The polymer phase transition depends on ionic strength and is sensitive to some detergents at high concentration. Guanidinium and phenol carryover block it. Before capture, ensure the lysate is at approximately physiological salt (100 to 200 mM monovalent), neutral pH, and detergent under 1 percent. If you used a chaotropic stabiliser, do a quick buffer exchange (spin column or dilution) first. This single step accounts for most of the "low yield" reports we receive.

Matching prep to the downstream question

Pre-capture checklist

• Sample stabilised or processed cold and fast
• RNase inhibitor present
• Debris removed by centrifugation
• Proteinase K for protein-rich samples, heat-inactivated
• Lysate at physiological salt, neutral pH, low detergent; no chaotrope carryover
• Low-titre samples concentrated
• Integrity checked on a representative sample

Get these right and the capture step is the easy part.