DeepCatch™ Small RNA Isolation Kit
Recover small and ultra-short RNA fragments that conventional methods often miss.
The DeepCatch™ Small RNA Isolation Kit combines phenol/chloroform phase separation with proprietary DeepCatch™ magnetic bead enrichment to isolate small RNA from tissues, cells, exosomes, yeast, bacteria, and other biological samples. The kit provides user-selectable recovery down to 15 nt in Standard Mode or down to 10 nt in Discovery Mode, with the flexibility to retain total RNA or reduce longer RNA background for small RNA enrichment. Purified RNA is compatible with downstream RT-qPCR, adapter ligation, small RNA profiling, and NGS library preparation.
PRODUCT OVERVIEW
Carrier-Free Recovery of Ultra-Short RNA Down to 10 nt
Breaks the conventional carrier trade-off—preserving ultra-short RNA without retaining the abundant background.
Recovering RNA fragments below 20 nt remains challenging (see DeepCatch™ Technology Fig 1). Conventional workflows often depend on abundant tRNA, rRNA, or added carriers to co-recover a limited fraction of ultra-short RNA. Removing these background species can also remove the ultra-short targets, while retaining them increases sample complexity, consumes library-preparation and sequencing capacity, and may promote adapter-dimer formation.
DeepCatch™ breaks this trade-off through direct, carrier-free capture. It enriches ultra-short RNA from the original sample while reducing longer RNA background, enabling recovery down to 10 nt with improved signal-to-noise (Fig. 1). No carrier RNA, glycogen, LPA, or similar additives are required.
One Kit, Two Flexible Workflows
Many commercial miRNA isolation kits can recover small-RNA-containing total RNA, but preparing a separate small-RNA fraction may require additional columns, an additional kit, or twice the consumables per sample. The DeepCatch™ kit is designed differently. The included reagents seamlessly support either total RNA purification or separate small-RNA fractionation, all without reducing the number of samples that can be processed.
Recover the Small RNAs Others Miss
User-selectable lower size limit for standard profiling or ultra-short RNA discovery.
KEY BENEFITS
Designed for small RNA recovery, enrichment, and downstream compatibility
- Ultra-short RNA recovery down to 10 nt (see DeepCatch™ Technology Fig 1)Efficiently recover small and ultra-short RNA fragments that are often lost using conventional RNA isolation methods.
- Flex-Range recovery options (see DeepCatch™ Technology Fig 3)Choose recovery down to 15 nt for conventional small RNA profiling or down to 10 nt for discovery applications.
- Broad sample compatibilityDesigned for tissues, cells, exosomes from plasma, serum, urine, cerebrospinal fluid, yeast, bacteria, and other biological samples.
- Carrier-free RNA capture (see DeepCatch™ Technology Fig 2)No carrier RNA, glycogen, linear polyacrylamide, or other nucleic acid carriers are required. This reduces artificial background and improves downstream compatibility.
- Reduced longer RNA background (Fig 1)An integrated enrichment step reduces a large portion of longer RNA fragments, increasing the relative abundance of small and ultra-short RNA in the final eluate.
- NGS-compatible output (see DeepCatch™ Technology Fig 5A, 5B)Purified RNA is suitable for RT-qPCR, adapter ligation, small RNA profiling, and NGS library preparation.
Recovery Modes
Select the RNA recovery range that fits your study.
| Mode | RNA Size Range | Recommended Use |
|---|---|---|
| Standard Mode | ≥15 nt | For conventional small RNA profiling where fragments below 15 nt are not required |
| Discovery Mode | >10 nt | For broader recovery of ultra-short RNA fragments, including 10–15 nt species |
Advanced Option: Pair with Fractionation Kit
Start with broad small RNA recovery, then add precision fractionation for focused ultra-short RNA analysis.
For applications requiring more precise size selection or stronger depletion of longer RNA species such as tRNA, purified RNA from this kit can be further processed with the DeepCatch™ Small Nucleic Acid Fractionation Kit (See Fig 1, Lane 4,5).
This dual-kit workflow enables targeted enrichment of the 10–40 nt RNA fraction and can reduce tRNA and other background species, improving signal-to-noise for small RNA expression profiling and NGS.
Performance Data
DeepCatch™ Small RNA Isolation Kit Preserves Ultra-Short Targets with Reduced tRNA Background
DeepCatch™ Small RNA Isolation Kit maximizes ultra-short fragment recovery while minimizing non-informative tRNA background
An input sample (Lane 1) comprising bacterial total RNA (prepared via acid-phenol/chloroform phase separation followed by isopropanol precipitation), spiked with three synthetic miRNAs (17 nt, 21 nt, and 25 nt) and a 12 nt ssDNA marker, was utilized to evaluate primary extraction efficiency and background depletion. The input was processed using either the DeepCatch™ Small RNA Isolation Kit (Lane 2) or a leading commercial isolation kit employing its large-fragment depletion protocol (Lane 3). The DeepCatch™ kit effectively removed larger RNA species, partially depleted the highly abundant tRNA population, and successfully retained all ultra-short fragments down to 12 nt. Conversely, although the leading competitor kit removed larger fragments, it failed to deplete the tRNA background and completely lost the 17 nt and 12 nt species during extraction.
To remove the vast majority of the remaining tRNA, both of the purified eluates were further processed using the DeepCatch™ Small Nucleic Acid Fractionation Kit (Cat# GM1048) (Lanes 4 and 5, corresponding to inputs from Lanes 2 and 3, respectively). (Note: The absence of the 17 nt and 12 nt fragment in Lane 5 is due to its absolute loss during the initial extraction step by the leading competitor kit in Lane 3).
These results demonstrate that the DeepCatch™ Small RNA Isolation Kit provides a vastly superior primary recovery of ultra-short targets with inherently cleaner background profiles. Analyzed on a 15% denaturing urea-PAGE with SYBR staining.
Fig. 1. DeepCatch™ Small RNA Isolation Kit recovers ultra-short nucleic acid targets while reducing tRNA background. Bacterial total RNA spiked with synthetic miRNAs (17, 21, and 25 nt) and a 12 nt marker was used as input (Lane 1). Extraction using the DeepCatch™ Small RNA Isolation Kit (Lane 2) successfully recovered all ultra-short fragments down to 12 nt while partially depleting the tRNA background. In contrast, a leading commercial column kit utilizing its large-fragment depletion protocol (Lane 3) failed to reduce the abundant tRNA background and suffered a loss of the 17 nt and 12 nt fragments. Further processing with the DeepCatch™ Fractionation Kit (Cat# GM1048) (Lanes 4 and 5) effectively depleted the remaining tRNA. The absence of the 17 nt and 12 nt fragments in Lane 5 highlights that these targets were permanently lost during the competitor's initial extraction step. (15% Urea-PAGE, SYBR staining).
Target RNA Classes
Capture a broader small RNA landscape. The DeepCatch™ Small RNA Isolation Kit supports the recovery and analysis of multiple short RNA classes, including:
| RNA Class | Typical Relevance |
|---|---|
| microRNAs | Gene regulation, expression profiling, biomarker research |
| piRNAs | Germline biology, genome regulation, disease research |
| tRNA-derived fragments | Stress response, cancer biology, extracellular RNA studies |
| snoRNA-derived fragments | Regulatory RNA biology and biomarker discovery |
| Y RNA fragments | Cell-free RNA research and liquid biopsy applications |
| Other ultra-short RNA fragments | Discovery-oriented small RNA and fragmentomics studies |
Applications
- Small RNA profilingRecover miRNAs, piRNAs, tRFs, Y RNA fragments, snoRNA-derived fragments, and other short RNA species.
- Ultra-short RNA biomarker discoveryAccess short RNA fragments down to 10 nt that may be missed by conventional RNA isolation methods.
- Exosomal and extracellular RNA analysisIsolate small RNA from exosomes derived from plasma, serum, urine, cerebrospinal fluid, and other biological fluids.
- Tissue and cell small RNA analysisRecover small RNA from tissue and cell samples using a robust phase-separation-based workflow.
- Small RNA NGS optimizationReduce longer RNA background and increase the fraction of informative small RNA reads.
- RT-qPCR and targeted assaysPrepare enriched small RNA input for sensitive downstream detection.
More than RNA isolation. Built for ultra-short RNA discovery.
Many RNA isolation workflows are optimized for total RNA or conventional small RNA, but they often under-recover fragments below 20 nt.
The DeepCatch™ Small RNA Isolation Kit extends small RNA recovery into the ultra-short range while maintaining a carrier-free, downstream-compatible workflow.
This makes it well suited for researchers who need cleaner, broader, and more complete small RNA recovery from challenging biological samples.