DeepCatch™ Flow-Through Short Nucleic Acid Recovery Kits
Rescue missed short nucleic acid fragments from conventional flow-through waste and other unbound fractions.
Conventional purification methods are highly effective for many standard nucleic acid applications. However, short nucleic acid fragments, such as miRNAs, tRFs, piRNAs, and ultra-short cfDNA/cfRNA, are frequently under-recovered and discarded with the flow-through. DeepCatch™ Flow-Through Recovery Kits use proprietary flexible-interface magnetic bead technology to capture these missed short-fragment fractions (Fig 1).
PRODUCT OVERVIEW
Turn discarded flow-through into a source of biological discovery
While standard kits are optimized for capturing total RNA, small RNA, cfRNA, cfDNA, or related nucleic acid targets, significant size-dependent loss is consistently observed across the 10–35 nt range (Fig 1). This discarded fraction holds critical biological information that is often lost before downstream analysis even begins.
By integrating a DeepCatch™ recovery step into your existing workflow, you can rescue these underrepresented short nucleic acid species with high efficiency. The result is a more complete molecular profile without replacing your established primary extraction protocol.
Don’t discard your discovery
Your target may already be in the flow-through.
KEY BENEFITS
Built to recover what conventional workflows leave behind
- Recovery down to 10 nt (see DeepCatch™ Technology Fig 1, Lane 4) Recover short RNA and DNA fragments as small as 10 nt from upstream flow-through waste .
- Two matrix-specific workflows Recover short nucleic acids from both organic-extracted, protein-depleted flow-through and lysate-derived, protein-containing flow-through or post-binding supernatant.
- Carrier-free recovery (see DeepCatch™ Technology Fig 2) No carrier nucleic acids, PEG, glycogen, LPA, or related additives are required, reducing artificial background and carryover concerns.
- Seamless Workflow Integration (Fig 1) Add a dedicated recovery step to conventional purification workflows without replacing your primary extraction protocol.
- Downstream compatible output (see DeepCatch™ Technology Fig 5A, 5B) Recovered nucleic acids are suitable for RT-qPCR, qPCR, adapter ligation, small RNA profiling, NGS library preparation, and biomarker discovery.
Kit Selection Guide
Two matrix-specific workflows are available: one for organic-extracted flow-through and one for lysate-compatible unbound matrices. Choose the kit based on the upstream flow-through or supernatant.
| Kit Version | Target Flow-Through Source | Matrix Characteristics |
|---|---|---|
| Organic Extracted | Phenol/chloroform, acid-phenol, TRIzol™, QIAzol™, or similar organic extraction steps | Proteins and cellular contaminants are largely removed (protein-depleted aqueous flow-through) |
| Lysate Compatible | Flow-through/supernatant from Proteinase K digested plasma or serum, and post-binding supernatants from phenol-based lysis without phase separation. | Proteins, lipids, detergents, or chaotropic salts remain present in the flow-through or post-binding supernatant |
Performance Data
Rescue of Missed 10-35 nt Nucleic Acids from Conventional Flow-Through Waste
A custom synthetic nucleic acid marker panel ranging from 10 to 120 nt was utilized as the input control (Lane 1). The same input was first extracted using a leading commercial column kit (Lane 2). The flow-through waste generated from this column extraction was immediately processed using the DeepCatch™ Flow-Through Recovery Kit (Lane 3).
The leading column kit retained longer fragments efficiently but showed clear size-dependent loss of shorter nucleic acids. Loss became apparent around 35 nt, was pronounced below 30 nt, and was especially severe below 25 nt, with fragments below 15 nt being nearly absent from the column-kit eluate. DeepCatch™ recovered multiple short-fragment species from the column-kit flow-through waste, demonstrating that the discarded flow-through contains recoverable nucleic acids missed by conventional column-based purification.
Recovery of 10 nt and 12 nt fragments from this third-party flow-through waste was partial under these conditions. This result reflects recovery from a flow-through matrix that was not optimized for DeepCatch™ system. For high-efficiency recovery of 10-12 nt fragments, DeepCatch™ beads should be used with optimized DeepCatch™ binding buffer conditions (see DeepCatch™ Technology Fig 1, Lane 4).
Analyzed on a 15% denaturing urea-PAGE with SYBR staining.
Fig 1. Rescue of missed short nucleic acids from conventional flow-through waste.
A synthetic nucleic acid marker panel ranging from 10 to 120 nt was used as input (Lane 1). Lane 2 shows fragments recovered by a leading column-based kit from the same input. The discarded flow-through from Lane 2 was subsequently processed using the DeepCatch™ Flow-Through Short Nucleic Acid Recovery Kit (Lane 3). The leading column-based kit showed size-dependent loss beginning around 35 nt, with strong loss below 30 nt and near-complete loss below 15 nt. DeepCatch™ successfully rescued the underrepresented 10-35 nt fragments directly from flow-through waste, recovering the valuable short nucleic acid populations that would otherwise be lost. (15% Urea-PAGE, SYBR staining).
Applications
- Small RNA profiling Recover lost regulatory RNAs (miRNAs, siRNAs, tRFs) to build a complete small RNA expression profile.
- Biomarker discovery Rescue low-abundance, ultra-short RNA and DNA fragments from limited clinical or biological samples.
- NGS library preparation Provide enriched short-fragment inputs for precise ligation-based library prep and next-generation sequencing.
- RT-qPCR and qPCR analysis Deliver inhibitor-free templates for highly sensitive targeted amplification assays.
Don't throw away your most valuable data.
Conventional purification methods often leave behind the very fragments needed for advanced fragmentomics and small RNA discovery.
DeepCatch™ Flow-Through Recovery Kits transform your sample waste into a source of biological discovery, ensuring that low-abundance, ultra-short nucleic acid species are successfully captured and ready for downstream analysis.
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