DNA FFPE Tissue Kit for DNA Extraction 

Product Description

This kit employs a safe, non-toxic, and environmentally friendly deparaffinization solution along with an efficient lysis/de-crosslinking reagent, which can lyse and release trace DNA in paraffin embedded sections and tissues. The high-affinity magnetic beads used in the kit can adsorb nucleic acids in a high-salt buffer and release nucleic acids in a low-salt elution buffer, thereby achieving rapid separation and purification of nucleic acids. The obtained products has good integrity and amplifiability, suitable for downstream applications such as PCR, next-generation sequencing, hybridization capture, etc. This kit can be used with automated nucleic acid extraction instrument for high-throughput extraction.

Features

• Safe and non-toxic: Use eco-friendly and non-toxic dewaxing agents instead of traditional toxic xylene for dewaxing
• High yield and quality: The extracted product has a high yield and purity, with no inhibition for downstream applications, 

and the extraction effect is stable and reliable.

Mechanism and workflow :

FFPE DNA Extraction Protocol – Magnetic Bead Method

Optimized DNA Extraction from Paraffin-Embedded and Formalin-Fixed Tissues

This optimized FFPE DNA extraction protocol is designed for efficient purification of high-quality genomic DNA from:

• Paraffin sections (FFPE samples)
• Paraffin-embedded tissue blocks
• Formalin-fixed tissues

The method combines deparaffinization, proteinase K digestion, de-crosslinking, and magnetic bead-based nucleic acid purification, ensuring high yield and purity for downstream applications such as PCR, qPCR, NGS, and sequencing analysis.

Step 1 – Sample Pretreatment

A. DNA Extraction from Paraffin Sections

Use 0.5–5 paraffin sections (10 µm thickness, approx. 30 mm² tissue surface).

1. Scrape tissue into a 1.5 ml microcentrifuge tube.
2. Add 800 µl Deparaffinization Solution.
3. Vortex 5 seconds vigorously.
4. Incubate at 56°C for 5 minutes.
5. Vortex 15 seconds.
6. Proceed to lysis and nucleic acid binding.

This step ensures effective paraffin removal for optimal DNA recovery from FFPE tissue.

B. DNA Extraction from Paraffin-Embedded Tissue Blocks

1. Scrape approximately 10 mg tissue into a 1.5 ml tube.
2. Add 800 µl Deparaffinization Solution.
3. Vortex 5 seconds.
4. Incubate at 56°C for 5 minutes.
5. Vortex 15 seconds.

Continue with the DNA lysis step.

C. DNA Isolation from Formalin-Fixed Tissue

1. Cut ~10 mg tissue into small pieces.
2. Add 500 µl PBS.
3. Centrifuge at 12,000 rpm (13,500 × g) for 1 minute.
4. Discard supernatant.
5. Repeat washing step three times.

Proceed to lysis and DNA purification.

This process improves DNA extraction efficiency from formalin-fixed samples by removing residual fixatives.

Step 2 – Lysis, De-Crosslinking and Magnetic Bead DNA Binding

1. Add 40 µl Proteinase K.
2. Add 200 µl L/D Buffer.
3. Incubate at 56°C for 60–180 minutes (complete digestion).
4. Incubate at 90°C for 60 minutes (reverse formalin cross-linking).

Transfer approximately 220 µl digestion solution into a new tube.

⚠ Important: Avoid transferring the upper deparaffinization layer.

Optional RNA removal:

Add 2 µl RNase A (100 mg/ml), incubate 3–5 minutes at room temperature.

Magnetic Bead DNA Purification

1. Add 400 µl FB Buffer.
2. Add 300 µl magnetic beads.
3. Incubate 3 minutes at room temperature.
4. Place on magnetic rack for 2 minutes.
5. Discard supernatant.

This ensures strong DNA binding to magnetic beads for high-purity extraction.

Step 3 – Washing and DNA Elution

Washing Steps

• Add 500 µl WA Buffer → magnetic separation → discard supernatant.
• Repeat once.
• Add 500 µl 80% ethanol → magnetic separation → discard.
• Repeat once.

Air dry 5–10 minutes.

DNA Elution

1. Add 50–100 µl Elution Buffer.
2. Incubate at 55°C for 5 minutes.
3. Place on magnetic rack.
4. Transfer purified DNA to new tube.
5. Store at –20°C.

Applications

Purified DNA is suitable for:

• PCR
• qPCR
• NGS library preparation
• Mutation analysis
• Forensic DNA testing