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| Product Name | Magnetic Bead-Based cfDNA Extraction Kit (Plasma/Serum) |
| Catalog No. | DREK-0007 |
| Description | A magnetic bead-based circulating cell-free DNA (cfDNA) extraction kit specifically optimized for the recovery of short, fragmented DNA molecules from plasma and serum samples. The optimized binding buffer composition and silica-coated magnetic bead surface chemistry ensure preferential recovery of 150-200 bp mononucleosomal DNA fragments without bias toward longer genomic DNA. The kit includes a specialized proteinase K digestion step to release cfDNA from nucleoprotein complexes and protein carriers, maximizing recovery of both double-stranded and single-stranded cfDNA species. |
| Intended Use | Extraction of circulating cell-free DNA from human plasma or serum for liquid biopsy applications including non-invasive prenatal testing, cancer mutation detection and monitoring, organ transplant rejection surveillance, and minimal residual disease assessment. |
| Principle / Technology | Plasma or serum is treated with proteinase K to dissociate cfDNA from histone complexes and carrier proteins. A binding buffer optimized for short DNA fragments is added, and cfDNA binds to silica-coated magnetic beads under high-salt conditions. The bead-bound cfDNA is washed to remove plasma proteins, salts, and PCR inhibitors. Purified cfDNA is eluted in a low-volume, low-salt buffer suitable for direct use in library preparation. |
| Detection Method | Bioanalyzer or TapeStation high-sensitivity DNA assay for fragment size profiling; Qubit fluorometric dsDNA HS quantitation; qPCR for single-copy and multi-copy genomic targets; digital droplet PCR (ddPCR) for absolute quantification and recovery efficiency; NGS library yield and quality metrics |
| Sample Type | Human plasma (EDTA preferred; citrate acceptable; heparin not recommended due to PCR inhibition); human serum; other cell-free body fluids including urine supernatant and cerebrospinal fluid (protocol optimization may be required) |
| Performance Range / Specifications | Input volume: 1-4 mL plasma; cfDNA recovery from 2 mL normal plasma: typically 10-50 ng (donor-dependent); A260/A280: 1.6-1.9 (fragmented DNA characteristic); fragment size distribution: 140-180 bp peak (mononucleosome); <1% high-molecular-weight genomic DNA contamination; recovery efficiency: >85% for 170 bp DNA fragment, >70% for 150-500 bp range |
| Sensitivity / LOD | Limit of detection: recovers <1 ng cfDNA from 1 mL plasma; single-molecule recovery confirmed by digital PCR; mutation detection sensitivity of 0.1% variant allele frequency achievable with extracted cfDNA in NGS workflows |
| Specificity | Enriches mononucleosomal cfDNA fragments with peak at 150-180 bp; recovers both double-stranded and single-stranded cfDNA species; minimal high-molecular-weight cellular genomic DNA contamination (<1%); consistent fragment representation without GC bias verified by NGS |
| Reaction Conditions / Protocol | Centrifuge blood at 1,600g for 10 minutes to obtain plasma; centrifuge plasma at 16,000g for 10 minutes to remove residual cells and debris; transfer 1-4 mL clarified plasma; add proteinase K and digestion buffer; incubate at 60°C for 20 minutes; add binding buffer and isopropanol; add magnetic bead suspension; incubate 15 minutes with intermittent mixing; separate beads magnetically; wash once with wash buffer 1 and twice with wash buffer 2; air-dry beads; elute in 20-50 µL elution buffer at 56°C for 5 minutes; total protocol: approximately 60-90 minutes |
| Components / Formulation | Proteinase K solution (20 mg/mL), digestion buffer (Tris-HCl, EDTA, SDS), binding buffer (guanidine hydrochloride, sodium acetate, isopropanol), magnetic silica bead suspension optimized for small DNA fragments (50 mg/mL), wash buffer 1 concentrate (guanidine hydrochloride, Tris-HCl, NaCl, ethanol), wash buffer 2 concentrate (Tris-HCl, NaCl, ethanol), elution buffer (10 mM Tris-HCl pH 8.0, 0.05% Tween-20), magnetic separation rack; carrier RNA (optional, for ultra-low-input samples, not included) |
| Storage Conditions | Proteinase K at 2-8°C; all buffers at room temperature; magnetic bead suspension at 2-8°C; elution buffer stored at room temperature; protect buffers from light; avoid freeze-thaw of magnetic beads |
| Shelf Life | 18 months from date of manufacture; proteinase K solution stable for 12 months at 2-8°C after opening |
| Package Specifications | 50 preparations (up to 2 mL plasma per prep) and 200 preparations; all buffers, proteinase K, and magnetic beads included; magnetic rack sold separately |
| Product Form | Liquid buffers; silica-coated magnetic bead suspension; proteinase K in glycerol-containing storage buffer |
| Quality Control | Each lot validated with pooled normal human plasma: cfDNA recovery ≥80% compared to reference method; fragment size distribution verified by Bioanalyzer (140-180 bp peak); genomic DNA contamination <1% by qPCR of long amplicon (1 kb); no PCR inhibitors; lot tested with ddPCR for KRAS wild-type and G12D mutation spike-in models; endotoxin <0.05 EU/µL eluate |
| Key Features | Optimized for short, fragmented cfDNA recovery; minimal high-molecular-weight DNA contamination; low elution volume maximizes concentration for NGS input; Tween-20 in elution buffer reduces DNA binding to tube surfaces; magnetic bead format suitable for automation; validated for major NGS library preparation chemistries including those requiring sub-nanogram inputs |
| Purity | A260/A280: 1.6-1.9 (characteristic of fragmented DNA); genomic DNA contamination <1% by qPCR; protein contamination below Bradford assay detection |
| Concentration | Elution in 20-50 µL; cfDNA concentration 0.2-2.0 ng/µL from 2 mL normal plasma; concentration depends on donor health status and sample handling |
| Activity / Unit Definition | Not applicable for cfDNA extraction kits |
| Molecular Weight | Not applicable; cfDNA consists predominantly of ~150-200 bp mononucleosomal fragments with lesser amounts of dinucleosome and oligonucleosome fragments |
| Source / Origin | Silica-coated magnetic beads specifically surface-optimized for short DNA fragment capture; proteinase K from recombinant expression; all buffer components are molecular biology grade, nuclease-free certified |
| pH Range / Optimal pH | Digestion buffer pH 7.8-8.2; binding buffer pH 5.0-5.5; wash buffer 1 pH 6.0-6.5; wash buffer 2 pH 7.0-7.5; elution buffer pH 8.0-8.2 |
| Shipping Conditions | Ambient temperature for buffers and beads; proteinase K shipped with cold packs; standard courier acceptable |
| Expiration Date / Stability | 18 months shelf life; stability verified by real-time testing at 0, 6, 12, and 18 months including cfDNA recovery and fragment profile integrity; accelerated aging at 37°C for 30 days confirms performance maintenance; after opening, buffers stable for 12 months |
| Regulatory / Compliance | For research use only; not for diagnostic applications; suitable for translational research and clinical trial correlative studies; components manufactured under ISO 13485 quality management principles |
| Compatibility | Eluted cfDNA compatible with all major NGS library preparation kits including those for whole-genome, targeted panel, and whole-methylome sequencing; suitable for ddPCR and qPCR mutation detection assays; compatible with KingFisher Flex and other automated extraction systems |
| Recommended Buffer System | Tris-SDS proteinase K digestion buffer; guanidine hydrochloride-based binding buffer with pH optimized for short DNA fragment retention; Tris-Tween-20 elution buffer to minimize surface adsorption |
| Application Notes / Precautions | Process plasma within 4 hours of blood collection or store at -80°C; EDTA plasma is preferred; avoid heparin anticoagulation; do not vortex during binding step to preserve fragment integrity; minimize freeze-thaw cycles of plasma; for volumes >4 mL, process in multiple aliquots and pool eluates; use low-retention microcentrifuge tubes for eluate collection; magnetic bead pellet should be barely damp, not cracked, before elution |
| Batch-to-Batch Consistency | Between-lot cfDNA recovery CV <15% using standardized plasma pool; fragment size distribution peak variation ±5 bp between lots; binding capacity controlled at ≥100 ng cfDNA per preparation; residual genomic DNA contamination verified <1% per lot; proteinase K specific activity controlled per batch |
For research use only, not for clinical use.
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