Expected output
Clean, full-length mRNA in nuclease-free water — free of enzymes, NTPs, salts, and very short abortive transcripts — concentrated and ready for downstream formulation. Vision-verified magnet and wash steps reduce the well-to-well variability that normally drives inconsistent yield.
QC metrics & targets
| Metric | What good looks like |
|---|---|
| Purity (A260/A280) | ≈ 2.0 for clean RNA |
| Salt / organic carryover (A260/A230) | High ratio — low carryover |
| Integrity & size | Full-length confirmed, minimal degradation/truncation |
Vision verification: the magnet settle, supernatant removal, and ethanol washes are camera-confirmed — the exact steps where RNA is lost — so a cloudy aspirate or incomplete wash is caught mid-run.
Quality control
The cleaned plate is read on a Nanodrop (Nano 1000, 2× 1:40 dilution) for concentration and purity ratios, and on a Fragment Analyzer for integrity and size. The measured concentration drives the volume math for the next step.
Tuning the cleanup: bead-ratio variants
Bead-to-sample ratio is the main knob — a higher ratio retains smaller fragments (more yield, less stringent); a lower ratio is cleaner but loses small species.
| Variant | Ratio | When to use |
|---|---|---|
| Standard cleanup (default) | 1.8× | Routine full-length mRNA cleanup |
| High-recovery / low-input | 2.0–2.2× | Low-yield IVT or precious template |
| Stringent / small-fragment depletion | 1.0–1.4× | Aggressively drop abortive transcripts |
| Double / two-sided size selection | ~0.6× then ~1.8× | Remove both oversized species and small junk |