AllPrep DNA/RNA FFPE Kit

DNA and RNA purified using the AllPrep DNA/RNA FFPE Kit are of comparable quality to DNA and RNA purified using the QIAamp FFPE Tissue Kit and RNeasy FFPE Kit/miRNeasy FFPE, respectively (see figure "Purification of DNA and RNA from FFPE samples"). The purified nucleic acids are therefore suitable for downstream applications such as Pyrosequencing or real-time PCR and RT-PCR (see figure "Reliable amplification of DNA and RNA from FFPE samples" and "Array analysis following preamplification of cDNA targets").

The AllPrep DNA/RNA FFPE Kit is specially designed for simultaneous purification of genomic DNA and total RNA from FFPE tissue sections. Pure DNA and RNA are obtained from the entire sample, in contrast to other procedures where the biological sample is divided into two before being processed separately. Simply dividing a sample in half for separate DNA and RNA purification procedures results in the purification of DNA and RNA from different populations of cells, which may differ in their properties. Purification of DNA and RNA from the same sample also helps to prevent waste, since FFPE samples are precious, often difficult to retrieve, and limited in amount.

Due to fixation and embedding conditions, nucleic acids in FFPE samples are usually heavily fragmented and are often of a lower molecular weight than those obtained from fresh or frozen samples. A major obstacle to isolating DNA and RNA from the same FFPE sample is that fragmented DNA is short and can be partly single-stranded and therefore more closely resembles RNA than intact DNA. This property of fragmented DNA makes physical separation of DNA and RNA difficult. The AllPrep DNA/RNA FFPE Kit uses a patent-pending solubilization method to differentially release DNA and RNA from a single FFPE sample.

Nucleic acids in FFPE samples are also chemically modified by formaldehyde. Although formaldehyde modification cannot be detected in standard quality control assays, such as gel electrophoresis or lab-on-a-chip analysis, it does strongly interfere with enzymatic analyses. The AllPrep DNA/RNA FFPE Kit is optimized to reverse as much formaldehyde modification as possible without further DNA and RNA degradation.

A simple workflow allows the purification of high-quality DNA and RNA from the same FFPE tissue section sample (see flowchart "AllPrep DNA/RNA FFPE procedure"). The AllPrep DNA/RNA FFPE Kit uses a patent-pending solubilization method to differentially release DNA and RNA from a single FFPE sample. With this method, FFPE samples are incubated in an optimized lysis buffer, which results in the release of RNA and precipitation of DNA. After centrifugation, the RNA-containing supernatant and DNA-containing pellet are then processed separately to purify RNA and DNA. Further incubations partially reverse crosslinking, and RNA or DNA is then purified using an RNeasy MinElute spin column or QIAamp MinElute spin column. For purified RNA, an on-column DNase treatment efficiently removes any contaminating DNA. Depending on the RNA binding conditions, small RNAs such as miRNA are either absent or present in the purified RNA. For purified DNA, an on-column RNase treatment is optional, as RNA contamination is minimal due to the separation of DNA and RNA prior to spin column processing.

The AllPrep DNA/RNA FFPE Kit is optimized to reverse as much formaldehyde modification as possible without further DNA and RNA degradation; however nucleic acids purified from FFPE samples should not be used in downstream applications that require high-molecular-weight DNA or full-length RNA. Some applications may require modifications to allow the use of fragmented nucleic acids (e.g., designing small amplicons for PCR and RT-PCR). For cDNA synthesis, gene-specific primers should be used instead of oligo-dT primers. If it is not possible to use gene-specific primers, random primers should be used.