cfDNA Purification Kit (Magnetic Beads)

The cfDNA Purification Kit (Magnetic Beads) was developed for cell free DNA (cfDNA) enrichment by separating genomic DNA contamination from isolated cfDNA samples.

Many diagnostic technologies for detection of disease signals in cfDNA begin with isolation and purification of DNA from liquid biopsy that include urine, plasma, cerebrospinal fluid. The most widely explored biotechnology is assays used to detect cancer-derived plasma cfDNA. Silica-based magnetic bead cfDNA isolation kits can reliably extract total DNA from plasma, but typically yield a large variation in cfDNA that includes the presence of genomic DNA that often depends on tumor stage, tumor size, or healthy status individuals. Most of the commercial cfDNA isolation kits can’t specifically recover the cfDNA while leaving the high molecular weight genomic DNA behind. The presence of genomic DNA can lead to decreased sensitivity or inconsistent results in downstream applications such as next-generation sequencing (NGS), PCR, QPCR, and digital PCR etc.

Therefore, an additional purification step to enrich cfDNA before downstream methods helps to improve signal from fragments that originate from cancer cells. A proportion of cancer-derived cfDNA fragment signals are below 100 bp and are often not detectable except by qPCR or single-stranded DNA based library preparation for NGS (1, 2, 3). Furthermore only 1% of cancer-derived fragments are found above 400 bp (1, 2). Capture of size-selected fragments between 90-150 bp improved detection of cancer by 2-4 fold (4). Furthermore, TF-bound and protected cfDNA fragments are also being investigated for active cancer-specific signals down to 35-80 bp (5, 6).

This kit uses Dual Solid Phase Reversible Immobilization (SPRI) technology for cfDNA purification. Most Dual SPRI procedures do NOT recover fragments below 100 bp. The kit can be used for the enrichment of cfDNA isolated from liquid biopsies, plasma, serum, and urine. The kit separates cfDNA (50-500 bp) and genomic DNA, and recovers of 90% of the cfDNA without the high molecular weight genomic DNA with high efficiency. Fragments at 500 bp and above may also be retained. Both the 50-500 bp and >500 bp DNA fractions can be used for downstream applications such as single-stranded or double stranded NGS library prep, qPCR, ddPCR, and other methods.

Features

• Separation of cfDNA and genomic DNA; Recovery of both types of DNA
• Recovery of cfDNA (50-500 bp)
  • As short as 50 bp can be recovered
• Recovery of high molecular weight genomic DNA
• Removal of unwanted components and other impurities
• Automation friendly

Examples of cfDNA purification. Both cfDNA and genomic DNA can be recovered separately.

The range of recovered small DNA fragments is from 50 to 500 bp. The input DNA are mixtures of sheared small DNA fragments and intact genomic DNA. The ratios of sheared DNA fragments versus genomic DNA are indicated.

Recovery rates of cfDNA and genomic DNA.

Many diagnostic technologies for detection of disease signals in cfDNA begin with isolation and purification of DNA from liquid biopsy that include urine, plasma, cerebrospinal fluid. The most widely explored biotechnology is assays used to detect cancer-derived plasma cfDNA. Silica-based magnetic bead cfDNA isolation kits can reliably extract total DNA from plasma, but typically yield a large variation in cfDNA that includes the presence of genomic DNA that often depends on tumor stage, tumor size, or healthy status individuals. Most of the commercial cfDNA isolation kits can’t specifically recover the cfDNA while leaving the high molecular weight genomic DNA behind. The presence of genomic DNA can lead to decreased sensitivity or inconsistent results in downstream applications such as next-generation sequencing (NGS), PCR, QPCR, and digital PCR etc.

Introduction

This kit provides fast purification of high-quality RNA from cells, tissues, and yeast using silica-membrane spin columns with a binding capacity of 100μg RNA. There is no need for phenol/chloroform extractions and time-consuming steps such as CsCl gradient ultracentrifugation or isopropanol precipitation. RNA purified using the HiPure Total RNA Purification System can be used for applications such as RT-PCR, Northern blotting, poly A+ RNA (mRNA) purification, nuclease protection, and in vitro translation.

Details

Specifications

Principle

The Kit isolates total RNA from up to 10⁷ cells or 20 mg tissue. A short workflow enables RNA isolation with genomic DNA removal in less than 25 mins. Samples are first lysed and homogenized. The lysate is passed through a DNA Mini column, ethanol is added to the flow-through, and the sample is applied to a RNA column. RNA binds to the membrane and contaminants are washed away. High-quality RNA is eluted in as little as 30µl water using the Kit.

Advantages

• Efficient removal of DNA – unique genomic DNA removal column without DNase treatment
• High quality – high purity total RNA can be directly used in various sensitive downstream applications
• Fast – several samples can be extracted in 25 minutes by column method
• Safe – no phenol chloroform extraction required
• Sensitive – RNA can be recovered at the level of PG

Kit Contents

Storage and Stability

HiPureKit can be stored dry at room temperature (15-25°C) and are stable for at least18 months under these conditions. During shipment, crystals or precipitationmay form in the Buffer RLC. Dissolve by warming buffer to 37°C.

This kit provides fast purification of high-quality RNA from cells, tissues, and yeast using silica-membrane spin columns with a binding capacity of 100μg RNA. There is no need for phenol/chloroform extractions and time-consuming steps such as CsCl gradient ultracentrifugation or isopropanol precipitation. RNA purified using the HiPure Total RNA Purification System can be used for applications such as RT-PCR, Northern blotting, poly A+ RNA (mRNA) purification, nuclease protection, and in vitro translation.