MagPure FFPE DNA/RNA Kit

MagPure FFPE DNA/RNA Kit (R6327) represents the magnetic bead co-extraction configuration within the Magen FFPE nucleic acid purification portfolio. The system is designed to recover both genomic DNA and RNA from formalin-fixed paraffin-embedded tissue samples using a magnetic adsorption workflow.

Following tissue digestion, nucleic acids are separated through magnetic bead binding behavior, allowing DNA and RNA fractions to be isolated during the adsorption stage. This configuration supports efficient recovery of fragmented nucleic acids typically present in FFPE samples and is optimized for Higher total DNA and RNA yield.

Magnetic particle chemistry and bead-to-lysate ratios were refined through internal development cycles to improve adsorption efficiency and recovery stability across different FFPE tissue conditions.

Laboratories prioritizing RNA integrity during extraction may refer to MagPure FFPE DNA/RNA Kit – IVD3026, where nucleic acid partitioning occurs earlier during the digestion stage.

Column-based purification workflows are available through HiPure FFPE DNA Kit – D3126 for genomic DNA extraction and HiPure FFPE RNA Kit – R4143 for RNA purification.

R6327 functions as the High-recovery magnetic reference workflow within the Magen FFPE extraction system.

Workflow

Workflow Overview

FFPE DNA/RNA Co-isolation Workflow II is based on a sequential magnetic adsorption strategy. After shared FFPE pretreatment and lysis, DNA is first captured by magnetic particles. The RNA-containing supernatant is then transferred into a second magnetic binding route for RNA purification. This staged adsorption design allows both DNA and RNA to be recovered from a shared FFPE lysate system through sequential magnetic binding.

Sample Handling Logic

The central partition point in this workflow is not physical pellet/supernatant separation at the early pretreatment stage, but the first DNA adsorption step. DNA is captured first, while RNA remains in the supernatant and is subsequently recovered through a separate magnetic binding route. This strategy is useful when the workflow objective is efficient same-sample recovery of both DNA and RNA, especially for parallel analysis or multi-omics-oriented applications.

Time and Workflow Characteristics

Under typical manual operation, the sequential adsorption workflow represented by R6327 usually requires about 3.3–14.5 hours, with the longer range mainly reflecting sample-dependent digestion before sequential magnetic binding. Because both DNA and RNA are recovered through staged adsorption, workflow completion should be interpreted based on the processing of both analyte routes. 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

Formalin fixation introduces crosslinks between nucleic acids and proteins, while paraffin embedding introduces hydrophobic contaminants that complicate nucleic acid recovery. In addition, nucleic acids extracted from FFPE tissues are typically fragmented due to fixation and long-term storage.

In the MagPure FFPE DNA/RNA workflow, tissue sections are first deparaffinized and digested with Proteinase K to release nucleic acids from the FFPE tissue matrix. A high-temperature incubation step is included to partially reverse formaldehyde crosslinking, improving accessibility of both DNA and RNA molecules.

Unlike conventional nucleic acid purification workflows where DNA or RNA is extracted separately, the MagPure FFPE DNA/RNA Kit uses a sequential magnetic adsorption strategy to isolate both nucleic acid types from the same lysate.

Genomic DNA is first captured by magnetic particles under optimized binding conditions. The remaining supernatant containing RNA is then transferred to a second adsorption step where RNA molecules bind to a separate magnetic particle system.

This staged adsorption design enables efficient recovery of both DNA and RNA from a single digestion process while maintaining compatibility with fragmented nucleic acids commonly present in FFPE tissues.

Engineering Characteristics

Magnetic Particle Adsorption

Silica-coated magnetic particles provide efficient adsorption of fragmented DNA and RNA commonly present in FFPE tissue lysates.

DNA/RNA Co-Isolation Workflow

The workflow enables recovery of both nucleic acid types from a single digestion process, supporting multi-omics analysis from limited FFPE tissue material

Fragment Recovery Performance

Magnetic bead binding conditions support recovery of short and degraded nucleic acid fragments typical of formalin-fixed tissues.

Low-Input Sample Recovery

Optimized bead-to-lysate ratios improve adsorption efficiency when processing low-concentration FFPE lysates.

Technical Validation

The performance of the DNA/RNA co-extraction workflow was evaluated through internal validation experiments together with external testing data generated under routine laboratory conditions.

Recovery Consistency and Production Stability

Internal evaluation using FFPE lysates with varying nucleic acid concentrations demonstrated consistent recovery across replicate extractions. In parallel, magnetic particle physicochemical parameters and extraction performance remained stable across validated production batches, supporting reproducible workflow performance.

RNA Integrity and PCR Compatibility

Electrophoresis analysis showed intact RNA bands without detectable degradation, including samples stored overnight at 4 °C after extraction. RT-PCR experiments further demonstrated comparable amplification efficiency between extracted RNA and reference controls, indicating effective removal of inhibitors that could affect downstream amplification.

Customer Sample Validation

Further validation was obtained from routine testing data generated in a leading oncology testing laboratory using FFPE specimens processed with the DNA/RNA co-extraction workflow.

In this dataset, qualified DNA results were obtained in 135 of 139 samples, while qualified RNA results were obtained in 114 of 116 samples. These results demonstrate reliable recovery performance for both analytes across routine FFPE sample testing workflows.

The evaluated specimens covered multiple common FFPE sample types, including surgical tissue, biopsy-derived samples and wax roll materials, supporting the applicability of the workflow across typical pathology laboratory inputs.

These findings provide additional evidence that the system is suitable for downstream molecular analysis workflows requiring FFPE-derived DNA and RNA from archived clinical specimens.

Kit Contents

Storage and Stability

Proteinase K, MagPure Particles N and MagBind Particles 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 at room temperature (15–25°C) and are stablefor at least 18 months under these conditions.

Experiment Data

For guidance on selecting the most appropriate FFPE nucleic acid extraction system based on target analyte, workflow format and downstream application requirements:

👉 FFPE Nucleic Acid Extraction Purchase Guide

For a broader technical overview of FFPE DNA, RNA and DNA/RNA co-extraction workflow routes, processing logic and application-oriented route design:

👉 FFPE Nucleic Acid Extraction Workflows Explained

For detailed workflow structure, estimated processing time and route-specific handling logic across representative FFPE workflows: