HiPure Circulating DNA Kit

Magen has been developing nucleic acid extraction technologies for over ten years, with a consistent focus on membrane-based purification systems. The HiPure Circulating DNA Kit (IVD3182) represents the column-based format within the circulating DNA portfolio, designed for plasma and serum workflows ranging from 1–5 mL input volumes.

The kit utilizes a vacuum-assisted silica membrane purification system optimized for recovery of low-abundance circulating DNA fragments while maintaining stable filtration performance. Membrane architecture and binding buffer formulation have been refined through internal optimization and validation experiments.

In internal verification testing, short DNA fragment recovery efficiencies typically exceeded 80% under controlled extraction conditions. Plasma extraction experiments using 5 mL input volumes showed stable cfDNA concentrations across replicate samples, with performance comparable to established column-based circulating DNA purification systems processed under equivalent conditions.

· Laboratories operating different workflow formats may refer to:

· Smaller plasma volumes 0.6mL→ ( D3180 )

· 1mL processing → ( D3181 )

· Centrifuge-based workflow → ( D3182D )

· Magnetic bead automation → ( IVD5435 )

Workflow

Workflow Overview

The HiPure Circulating DNA Kit uses a silica column–based workflow for purification of circulating DNA from plasma and serum samples. Following carrier RNA–assisted lysis, DNA is captured on the silica membrane under optimized binding conditions and recovered through washing, drying and elution steps. This workflow provides a structured and reproducible approach for routine cfDNA extraction. A centrifugation-based variant is available as D3182D for laboratories that prefer spin-based handling over vacuum processing.

Sample Handling Logic

The workflow is designed for 1–5 mL plasma or serum input, with the main variation concentrated in the lysis and binding stages under larger-volume handling. Once DNA binding conditions are established, the downstream column purification steps remain consistent, enabling stable performance across routine sample conditions.

Time and Workflow Characteristics

Under typical manual operation, the overall workflow is usually completed within about 65–80 minutes, depending mainly on sample input volume and lysis conditions. For detailed step-by-step conditions, workflow guidance and estimated processing times, please refer to the Workflow Note in the Download section.

Specifications

Extraction Principle

The HiPure Circulating DNA Kit is designed for purification of circulating cell-free DNA (cfDNA) from plasma, serum, or urine samples. Circulating nucleic acids in biological fluids are typically present at low concentrations and often exist as short DNA fragments.

Samples are lysed using a chaotropic buffer together with Proteinase K to release nucleic acids from protein complexes and protect DNA from degradation. Carrier RNA is included to improve recovery efficiency of low-abundance DNA molecules.

Under optimized binding conditions, circulating DNA fragments bind to the silica membrane of the HiPure cfDNA column while proteins and other contaminants pass through during filtration. After sequential washing steps to remove residual impurities, purified DNA is eluted in a low-salt buffer suitable for downstream molecular analysis workflows.

Engineering Characteristics

Optimized Column Membrane Architecture

Internal evaluation of different membrane configurations showed that a three-layer silica membrane structure provided an effective balance between DNA adsorption efficiency and filtration time during cfDNA extraction.

Binding Buffer Optimization

An updated binding buffer formulation (ACB) was developed to reduce solution viscosity during plasma processing. Internal testing showed that this modification improved filtration efficiency while maintaining comparable DNA recovery performance.

Designed for Large-Volume Plasma Processing

The column format supports processing of milliliter-scale plasma samples, enabling recovery of low-abundance circulating DNA molecules commonly present in clinical liquid biopsy samples.

System Integration

IVD3182 connects to a structured circulating DNA product framework:

• Low-volume plasma extraction → (D3180)

• Standard 1mL workflow → (D3181)

• Centrifuge processing → (D3182D)

• Scalable magnetic workflow → (IVD5435)

• Fragment selection workflows → (12927)

Technical Validation

Validation experiments were performed to evaluate recovery efficiency and reproducibility of the purification system.

Short DNA Recovery Testing

Marker recovery experiments demonstrated DNA recovery efficiencies generally exceeding 80%, confirming effective capture of fragmented DNA molecules typical of circulating nucleic acids.

Batch Consistency Testing

Batch-to-batch verification experiments showed stable DNA recovery performance across different production lots, with recovery rates consistently above 80% and minimal variation between tested batches.

Urine Sample Validation

Urine extraction experiments using spiked short DNA fragments demonstrated recovery efficiencies typically ranging from 84% to 102% under optimized extraction conditions.

Customer Sample Validation

Performance was further evaluated using 46 customer plasma samples processed with the HiPure Circulating DNA Kit under routine testing conditions at a leading oncology testing company. Among these samples, 45 were assessed as qualified and 1 as risk, indicating stable extraction performance across real-world sample inputs.

Sample input volumes ranged from 3.0 mL to 6.5 mL, with most workflows centered around 4.5-5.0 mL plasma. These results support the suitability of the system for circulating DNA extraction from clinically relevant plasma volumes.

Fragment Size Recovery

Circulating cell-free DNA molecules are typically fragmented and often fall within the nucleosomal DNA size range.

Fragment recovery experiments using short DNA markers confirmed that the purification system can capture fragments around 50 bp in length with recovery efficiencies above 80%.

Analysis of circulating DNA extracted from serum samples showed fragment distributions typically ranging between approximately 150 bp and 1000 bp, consistent with reported cfDNA fragment characteristics.

These results indicate that the purification chemistry supports recovery of fragmented circulating DNA suitable for downstream molecular analysis.

Performance Comparison

Comparative extraction experiments were performed using plasma samples processed with the HiPure Circulating DNA Kit and a widely used commercial cfDNA extraction system.

In testing using 5 mL plasma samples, Qubit quantification indicated that DNA concentrations obtained with the HiPure system were comparable to or higher than those obtained with the reference column-based extraction kit in several replicate samples.

Downstream library preparation experiments demonstrated that extracted DNA supported adapter ligation and PCR amplification workflows used for sequencing library construction.

Kit Contents

Storage and Stability

Proteinase K, Carrier RNA should be stored at 2-8°C upon arrival. However, short-term storage (up to 12 weeks) at room temperature (15-25°C) does not affect their performance. The remaining kit components can be stored dry at room temperature (15-25°C) and are stable for at least 18 months under these conditions. The entire kit can be stored at 2-8°C, but in this case buffers should be redissolved before use. Make sure that all buffers are at room temperature when used.

Experiment Data

For guidance on selecting the most appropriate DNA extraction system based on sample type, input volume and workflow requirements:

👉 Magen Kits Selection Guide

For a broader technical overview of cfDNA workflow routes, processing logic and downstream application orientation:

👉 cfDNA Extraction & Enrichment Workflows

For reference workflow structure and comparative processing logic across representative cfDNA workflows:

👉 cfDNA Workflow Notes (IVD3182 / IVD5435 / 12927)

Related cfDNA Application Notes: These application notes help explain how this circulating DNA extraction route fits different plasma cfDNA research workflows and downstream assay requirements.

👉 Application Map · Oncology ctDNA · Methylation Biomarkers