riboLASSO vs. Other rRNA Depletion Methods
Team Dynamic Matrices | 17 July 2026
Most rRNA depletion kits on the market today, including NEBNext® (New England Biolabs), riboPOOLs™ (siTOOLs Biotech), RiboCop® (Lexogen), Illumina Ribo-Zero® Plus, Zymo-Seq RiboFree™ (Zymo Research), and NEXTFLEX® RiboNaut™ (Revvity), rely on one of a few mechanisms that have been the industry standard for over a decade: biotinylated probe hybridization with magnetic bead pulldown, RNase H enzymatic digestion of RNA:DNA hybrids, or probe-free enzymatic depletion. riboLASSO takes a different approach, using DNA-crosslinked polymer capture instead of beads or enzymes. Here's how they compare, both by mechanism and against each of these named kits directly.
Mechanism & key features
| Feature | riboLASSO | Conventional Methods (Probe/Bead or RNase H) |
|---|---|---|
| Depletion mechanism | DNA-crosslinked polymer network that selectively engulfs rRNA through a phase-change reaction, forming a separable pellet. | Biotinylated probes hybridize to rRNA and are pulled down with streptavidin magnetic beads, or RNase H digests the RNA strand of an RNA:DNA hybrid. |
| Beads required | No. Bead-free. | Yes, for bead-based methods. RNase H methods don't need beads but do need enzyme and a heat-inactivation step. |
| Enzyme dependency | None. | RNase H or DNase required for enzymatic digestion methods. |
| Depletion efficiency | Consistent, above 98%. | Typically high on intact RNA, but depends on probe panel coverage and enzyme performance. |
| Binding capacity | Up to 1000 ng of total RNA. | Varies by kit and recommended input amount. |
Operation & sample handling
| Feature | riboLASSO | Conventional Methods (Probe/Bead or RNase H) |
|---|---|---|
| Sample recovery | Pellet recovered by centrifugation. No magnetic rack needed. | Magnetic rack required for bead-based separation. |
| Protocol time | 40–60 minutes total. Under 5 minutes of hands-on time per sample, or about 15 minutes hands-on for a batch of 24 samples. | Varies by kit; probe hybridization and bead-wash workflows commonly run longer, with more manual handling steps. |
| High-throughput format | Pre-mixed and pre-aliquoted versions can be made available on request for large-scale applications. Request a format → | Format flexibility varies by vendor. |
| Degraded or low-input RNA | Performance data is currently under validation. Register to be notified when it's available → | Performance can decline, since both probe hybridization and enzymatic digestion are sensitive to RNA integrity. |
| Library bias | Lower-bias libraries, since there's no solid-phase binding step. | Solid-phase (bead) binding can introduce its own bias. |
Applications & coverage
| Feature | riboLASSO | Conventional Methods (Probe/Bead or RNase H) |
|---|---|---|
| Species coverage | Currently configured for human total RNA. Other organisms via LASSOflex's custom catcher strand design. | Broader out-of-box species catalogs are available from established vendors, a genuine advantage of methods with a longer track record. |
| Off-target reads | Up to 7× fewer off-target outliers than beads or enzymes. | Residual rRNA and off-target binding are a well-documented source of wasted sequencing depth. |
Cost & storage
| Feature | riboLASSO | Conventional Methods (Probe/Bead or RNase H) |
|---|---|---|
| Relative cost | Less than half the price of state-of-the-art kits. | Reference point for the comparison above. |
| Storage | Stable for approximately 1 year at 4°C. | Many established kits require -20°C storage. |
Performance and cost figures reflect current internal data; a peer-reviewed reference will be linked here once published.
riboLASSO vs. named rRNA depletion kits
| Kit (vendor) | Mechanism | Enzyme / bead use | Input range | Workflow time |
|---|---|---|---|---|
| riboLASSO (Dynamic Matrices) | DNA-crosslinked polymer capture, phase-separated pellet | Bead-free, enzyme-free | ~1–1000 ng total RNA | 40–60 min total, <5 min hands-on/sample |
| NEBNext® rRNA Depletion Kit v2 (NEB) | RNase H digestion of RNA:DNA hybrids | RNase H + DNase enzymes, no beads | 10 ng–1 µg | ~2 hours, <10 min hands-on |
| riboPOOLs™ (siTOOLs Biotech) | Biotinylated probe hybridization | Streptavidin magnetic beads, no enzyme | 100 ng–5 µg | Not publicly specified |
| Zymo-Seq RiboFree™ (Zymo Research) | Probe-free enzymatic cDNA-hybrid removal | Enzymatic, no probes or beads | 100 ng–2 µg (50 ng from ribo-depleted RNA) | As little as 3.5 hours (full library prep) |
| RiboCop® (Lexogen) | Probe-based affinity capture | Enzyme-free | 1 ng–1 µg | ~1.5 hours |
| Ribo-Zero® Plus (Illumina) | Enzymatic depletion | Enzyme-based, no beads | 1–1000 ng (10–100 ng optimal) | ~40 minutes |
| NEXTFLEX® RiboNaut™ (Revvity) | Subtractive hybridization | Streptavidin magnetic beads, no enzyme | 5 ng–1 µg | ~9–10 hours |
Competitor specifications are sourced from each vendor's own published product documentation as of September 2026 (see References below) and may change; riboLASSO figures reflect current internal data, as noted above.
None of this makes probe- and enzyme-based kits obsolete. They have years of published validation behind them and, for now, cover far more organisms out of the box than riboLASSO does. Where riboLASSO earns its place is in the specific situations those methods handle least gracefully: degraded RNA, low-input samples, and workflows where a bead-free, enzyme-free mechanism removes a source of variability from the experiment.
References
- New England Biolabs. NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat). Product documentation.
- siTOOLs Biotech. riboPOOLs™ for ribosomal RNA depletion. Product documentation.
- Zymo Research. Zymo-Seq RiboFree™ Total RNA Library Kit. Product documentation.
- Lexogen. RiboCop® rRNA Depletion Kit. Product documentation.
- Illumina. Ribo-Zero® Plus rRNA Depletion Kit. Product documentation.
- Revvity. NEXTFLEX® RiboNaut™ rRNA Depletion Kit (HMR). Product documentation.
NEBNext®, riboPOOL™, RiboCop®, Ribo-Zero®, Zymo-Seq RiboFree™, and NEXTFLEX® RiboNaut™ are trademarks of their respective owners. Dynamic Matrices is not affiliated with or endorsed by these companies.
FAQs
For most standard human total RNA workflows, yes. riboLASSO works directly on total RNA and fits into standard library prep, without a magnetic rack or enzyme incubation step.
Not yet. The current riboLASSO kit is configured for human total RNA. Established probe- and enzyme-based kits currently offer broader out-of-box species coverage. For other organisms, LASSOflex allows a custom catcher strand to be designed through the pilot program.
riboLASSO differs from all three in mechanism. NEBNext® depends on RNase H enzymatic digestion, riboPOOLs™ use biotin-streptavidin magnetic bead pulldown, and RiboCop® uses an enzyme-free probe-based workflow. riboLASSO instead uses DNA-crosslinked polymer capture, needing neither an enzyme nor a magnetic bead step. See the comparison table above for input range and workflow time for each.
Yes, for standard human total RNA depletion. Both Ribo-Zero® Plus and Zymo-Seq RiboFree™ use enzymatic mechanisms rather than riboLASSO's bead-free, enzyme-free polymer capture. See the comparison table above for their respective input ranges and workflow times.