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Streamline Your DNA Extraction
from FFPE and FNA Samples
Streamline Your DNA Extraction from FFPE and FNA Samples
Introduction
Formalin fixation and paraffin embedding (FFPE) tissues and fine needle aspiration (FNA) biopsy samples are popular sources of archival tissue samples used in cancer research and diagnosis. However, extracting high-quality genomic DNA from FFPE tissues and FNA samples is challenging due to the cross-linking between proteins and DNA caused by formalin fixation. In this blog post, we will discuss the importance of high-quality genomic DNA for molecular oncology diagnostics, the challenges in DNA extraction from FFPE tissues and FNA samples, and how the BcMag™ One-Step FFPE & FNA DNA Purification Kit can simplify this process.
Challenges in DNA extraction from FFPE tissues and FNA samples
Extracting high-quality genomic DNA from FFPE tissues and FNA samples is a challenge due to the cross-linking between proteins and DNA caused by formalin fixation. This process causes extensive DNA damage and fragmentation, which can cause problems in downstream applications that use PCR. Additionally, commercially available nucleic acid extraction kits require a minimum of one 10µm slide of starting material, limiting the number of feasible applications and the potential for significant DNA loss during the extraction procedure.
To address these limitations, the BcMag™ One-Step FFPE & FNA DNA Purification Kit has been designed to efficiently extract total nucleic acids from 2µm – 5µm FFPE tissue or FNA samples. This enables researchers to extract DNA from smaller tissue samples, increasing the number of feasible applications. Additionally, the proprietary magnetic beads used in this kit can remove PCR inhibitors from the samples in a single step without the need for DNA extraction. This leads to increased nucleic acid yields and reduces the risk of DNA loss due to the “Bind-Wash-Elute” procedure used in traditional DNA purification techniques.
Workflow of One-Step FFPE & FNA DNA Purification and DNA purification results
1.
Add functional magnetic beads and proteinase K to the sample and incubate at 65°C.
2.
Vortex/pipette the beads with the sample to capture the PCR inhibitors.
3.
Separate the beads from the sample using a magnet.
4.
Aspirate the supernatant containing the pure, ready-to-use DNA/RNA.
Advantages and Benefits
Fast and Efficient: The One-Step FFPE & FNA DNA Purification Kit is designed for efficient and fast extraction of total nucleic acids from FFPE tissues and FNA samples. The entire procedure can be completed in less than 30 minutes, and the kit can process more than 96 samples simultaneously.
High-Quality DNA
The kit utilizes unique magnetic beads that efficiently remove paraffin from FFPE tissue samples in an aqueous buffer while simultaneously rehydrating the tissue. The proprietary magnetic beads also remove PCR inhibitors from samples in a single step, which increases nucleic acid yields and avoids DNA loss caused by traditional DNA purification techniques. The purified genomic DNA has the highest integrity and purity, making it ideal for various downstream applications.
Improved Safety and Convenience
Traditional DNA extraction methods involve the use of toxic organic solvents, such as xylene or d-limonene, which are flammable and have an unpleasant odor. The One-Step FFPE & FNA DNA Purification Kit eliminates the need for these solvents, making the procedure safer and more convenient. Additionally, the kit simplifies the traditional “bind-wash-elute” procedure, reducing the risk of DNA loss and saving time.
High Compatibility
The purified genomic DNA from this kit is compatible with various downstream applications such as qPCR, mutation screening, microarray analyses, sequencing, Southern blotting, and SNP analysis. The high-quality DNA obtained from this kit can help increase the accuracy and sensitivity of downstream analyses, leading to more reliable results.
In summary
The one-step purification technique employed by the BcMag™ kit is straightforward and ideal for processing more than 96 samples simultaneously. The kit produces pure DNA in less than 30 minutes, making it a time-efficient option. Purified genomic DNA has the highest integrity and can be used in various downstream applications, including qPCR, mutation screening, microarray analyses, sequencing, Southern blotting, and SNP analysis. With this kit, researchers can achieve high-quality DNA extraction from FFPE and FNA tissues for use in a wide range of molecular oncology diagnostics.