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$455.00
Sku: 220501
Availability:
QUICK SHIP
In stock & estimated to ship in 1-2 days by April 28, 2026
The Biofargo cccDNA Purification Kit provides fast, enzyme-free isolation of covalently closed circular DNA (cccDNA) from total DNA samples — no Exonuclease III, Plasmid-Safe DNase, or T5 Exonuclease required. Designed for HBV cccDNA research, circulating eccDNA profiling, and cancer biomarker discovery from plasma, liver tissue, and cell models. Compatible with silica columns and magnetic bead workflows. 100 preps per kit. For research use only.
Description
Covalently closed circular DNA (cccDNA) is the natural topological form of most plasmids and a key replicative intermediate in viruses such as hepatitis B virus (HBV). In eukaryotes, cccDNA-like structures — known as extrachromosomal circular DNA (eccDNA) — play roles in innate immune signaling, cell-to-cell communication, genetic heterogeneity, gene dosage compensation, aging, and gene regulation. Cell-free eccDNAs in bodily fluids are emerging as promising non-invasive biomarkers for cancer diagnosis and prognosis.
Traditional cccDNA isolation relies on multiple rounds of enzymatic digestion (Exonuclease III, Plasmid-Safe DNase, Exonuclease I/III combinations, or T5 Exonuclease) to deplete linear and open-circular DNA, introducing risk of residual nuclease damage and protocol variability. This kit uses a proprietary, enzyme-free extraction chemistry that exploits the topological differences between circular and non-circular DNA — delivering high-purity cccDNA in a single streamlined step.
Key features
01
No enzymatic digestion
Eliminates residual nuclease risk that can nick or degrade purified cccDNA
02
One-step protocol
Streamlined workflow significantly reduces hands-on time vs. multi-enzyme methods
03
High recovery efficiency
Minimal contamination with linear or open-circular DNA forms
04
All cccDNA sizes
Broad compatibility — from small plasmid-sized cccDNA to large eccDNA species
05
Flexible format
Works with silica-based spin columns and magnetic bead systems
06
100 preps per kit
Sufficient for method development through moderate-throughput studies
Applications
Virology
HBV cccDNA research
Isolation of HBV cccDNA from infected hepatocytes, liver tissue biopsies, and in vitro cell models for antiviral drug studies
Oncology
Cancer biomarker discovery
Extraction of circulating eccDNA from plasma and serum for liquid biopsy, diagnostic, and prognostic research
Aging & Genetics
eccDNA profiling
Profiling eccDNA landscapes in aging models, cancer cell lines, and tissues to study heterogeneity and gene dosage
Genomics
Gene expression & sponging
Research into eccDNA-mediated regulation of gene expression and miRNA sponging mechanisms
High-throughput
DNA structure analysis
Large-scale cccDNA profiling by NGS or qPCR with reproducible, enzyme-free sample prep
Choose your kit — 220501 vs 220502
Both kits use the same enzyme-free workflow. The difference is what's included in the box.
Cat# 220501
Standard Kit
$455
$4.55 per prep · 100 preps
Extraction Solution A — 100 mL included
Extraction Solution B prepare in-house
Precipitation Solution prepare in-house
Enzyme-free, one-step protocol
Column & magnetic bead compatible
Cat# 220502
✓ Recommended
Extended Kit
$640
$6.40 per prep · 100 preps
Extraction Solution A included
Extraction Solution B included
Precipitation Solution included
Enzyme-free, one-step protocol
No additional reagent preparation needed
Full kit contents comparison
| Component / feature | 220501 Standard | 220502 Extended |
|---|---|---|
| cccDNA Extraction Solution A | ✓ 100 mL | ✓ 100 mL |
| cccDNA Extraction Solution B | — prepare in-house | ✓ included |
| cccDNA Precipitation Solution | — prepare in-house | ✓ included |
| Preps per kit | 100 | 100 |
| Enzyme-free workflow | ✓ | ✓ |
| Silica column compatible | ✓ | ✓ |
| Magnetic bead compatible | ✓ | ✓ |
| Storage | 4 °C · ≥1 year | 4 °C · ≥1 year |
| Best for | Labs that can prepare Solution B & Precipitation Solution in-house | Labs wanting a fully ready-to-use, self-contained kit — no extra reagent prep |
Not sure which kit fits your lab? Email contact@biofargo.com or call (804) 529-2296
Input sample requirements
⚠ Important — read before starting
- Recommended extraction method: SDS-proteinase K digestion followed by alcohol precipitation. Proteinase K releases cccDNA from protein covalent linkages; alcohol precipitation recovers both cccDNA and non-cccDNA non-exclusively.
- Process immediately or freeze: To prevent nicking by residual DNase, begin cccDNA purification immediately after total DNA isolation — or quick-freeze the total DNA preparation and store at −80 °C until ready.
- Solvent: Total DNA must be dissolved in DNase-free water or TE buffer. Other solvents may be incompatible — a trial experiment is required before use.
Storage and handling
Store at 4 °C · Stable for at least 1 year from date of receipt
References
- Wang Y, et al. Purification, full-length sequencing and genomic origin mapping of eccDNA. Nature Protocols, 2022.
- Wang Y, et al. eccDNAs are apoptotic products with high innate immunostimulatory activity. Nature, 2021.
- Wang M, et al. Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer. Int J Biol Sci 17(4): 1010–1025, 2021.
- Hirt B. Selective extraction of polyoma DNA from infected mouse cell cultures. J Mol Biol 26:365–369, 1967.
- van Loon N, Miller D, Murnane JP. Formation of extrachromosomal circular DNA in HeLa cells by nonhomologous recombination. Nucleic Acids Res 22(13):2447–2452, 1994.
- Gaubatz JW. Purification of eucaryotic extrachromosomal circular DNAs using exonuclease III. Anal Biochem 184(2):305–310, 1990.
- Werle-Lapostolle B, et al. Persistence of cccDNA during the natural history of chronic hepatitis B and decline during adefovir dipivoxil therapy. Gastroenterology 126:1750–1758, 2004.
- Kock J, et al. Generation of covalently closed circular DNA of hepatitis B viruses via intracellular recycling is regulated in a virus specific manner. PLoS Pathog 6:e1001082, 2010.
- Schnepp BC, et al. Genetic fate of recombinant adeno-associated virus vector genomes in muscle. J Virol 77:3495–3504, 2003.
- Luo J, et al. Identification of an intermediate in HBV covalently closed circular (ccc) DNA formation and sensitive and selective cccDNA detection. J Virol 91:e00539-17, 2017.
- Qu B, et al. T5 Exonuclease Hydrolysis of Hepatitis B Virus Replicative Intermediates Allows Reliable Quantification and Fast Drug Efficacy Testing of cccDNA by PCR. J Virol 92(23):e01117-18, 2018.
- Vinograd J, Lebowitz J. Physical and Topological Properties of Circular DNA. J Gen Physiol 49(6P2):103, 1966.
- Shibata Y, Kumar P, et al. Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues. Science 336(6077):82–86, 2012.
When can I expect my order to ship?
Most orders are filled and shipped within 2-3 business days from the time they are received.
Our standard shipping usually take 2-5 days.
We also provide express shippping for time-sensitive deliveries.
Email contact@biofargo.com if you have any requirements.
