DNA size selection (or DNA sizing) is a widely used analytical method in molecular biology, biochemistry, and microbiology. Specific applications of DNA sizing include microbial identification and discrimination, genotyping, and sequencing. Precise DNA sizing can improve sequencing efficiency, reduce cost, improve data quality, and even enable sequencing of low-input samples. Traditional DNA size selection approaches are mostly based on chromatography or electrophoresis, whose tedious operation limits their applications. Conventional gel electrophoresis using a solid polymer and a static electric field are routinely used to separate and size DNA fragments of ≤20 kb. Currently common DNA sizing methods cannot be used at high resolution (<20 bp) to differentiate DNA fragments below 200 bp.
MiniEnrich is a simple, automatable, high-resolution DNA size enrichment technique based on a magnetic nanoplatform. Two types of MiniEnrich magnetic nanoparticles were developed to filter high molecular weight DNA at high resolution and recover the remaining DNA fragments at the threshold of interest with a yield of 95%. The MiniEnrich technology can be used to facilitate monogenic disease detection or as a tool for applications involving differences in the size of DNA fragments.
The mixture containing DNA fragments of different sizes is first mixed with carboxyl nanoparticles (substrate A). Carboxyl nanoparticles capture DNA with a size over a defined threshold in the presence of polyethylene glycol (PEG) as a crowding agent. Then, the supernatant is separated from substrate A. The short fragments together with the impurities remaining in the supernatant are transferred to a new tube and mixed with hydroxyl nanoparticles (substrate B) in the presence of isopropanol. Hydroxyl nanoparticles effectively capture remaining DNA with a size below the defined threshold. DNA fragments captured on substrate A and substrate B are then washed and eluted individually, achieving enriched DNA above or below this defined size threshold.
Workflow for isolation of DNA fragments using MiniEnrich beads
Amerigo Scientific offers MiniEnrich Short Fragments Enrichment Kit for enrichment of DNA fragments through magnetic nanotechnology, a simple, automatable, high-resolution DNA size enrichment method. The kit contains two types of magnetic nanoparticles. One is the carboxyl nanoparticles that can filter high molecular weight DNA at high resolution, and the other is the hydroxyl nanoparticles that can recover the remaining DNA fragments below the size threshold of interest with a recovery of more than 95%. This kit is a new tool for high-resolution DNA enrichment below 200 bp and improves the accuracy of DNA detection.
|MiniEnrich Short Fragments Enrichment Kit||20 ul x 20 preps/kit; 20 μL x 50 preps/kit|
The MiniEnrich Carboxyl Beads for Size Selection are designed for size selection of DNA fragments from a mixture of DNA with various sizes and can be used for downstream analyses such as next generation sequencing (NGS) and other molecular biology. In the NGS library preparation workflow, the MiniEnrich Carboxyl Beads can be used on samples before or after DNA fragmentation, ligation, or library amplification. With the proprietary MiniEnrich technology, MiniEnrich Carboxyl Beads feature customized cut-off sizes, efficient removal of non-target fragments and recovery of target DNA fragments.
The MiniEnrich Carboxyl Beads for Purification are designed to purify DNA fragments from contaminants in NGS and molecular biology workflows. The MiniEnrich Carboxyl Beads can be used on samples after DNA isolation, fragmentation, PCR amplification, cloning, library preparation, etc. With the proprietary MiniEnrich technology, MiniEnrich Carboxyl Beads are more effective at removing contaminants and recovering DNA fragments of interest than current market-leading products.
|MiniEnrich Carboxyl Beads for Size Selection||30mL/bottle|
|MiniEnrich Carboxyl Beads for Purification||30mL/bottle|
MiniEnrich Size Selection Beads are used to precisely select DNA in narrower size range with less DNA residue of non-target fragments. As shown in Figure 1, more DNA fragments (<500 bp) of interest were recovered using MiniEnrich Size Selection Beads than using market-leading products. Figure 2 shows that the cut-off with good yield and resolution could be achieved by adjusting the ratio of magnetic beads to sample.
Figure 1. Less DNA residue using MiniEnrich Size Selection Beads. dsDNA step ladder (50-3000 bp) in TE buffer (red) was treated with MiniEnrich Size Selection Beads for left-side size selection (blue) or a magnetic beads-based market-leading product (green).
Figure 2. Beads to sample ratio adjusted for customized size selection. gDNA from Hela cells was fragmented (red) and MiniEnrich Size Selection Beads was used to select DNA fragments of interest.
MiniEnrich Purification Beads are designed to efficiently remove small fragments such as primer, primer-dimer, adaptor, and adaptor-dimer, as well as other contaminates such as dNTPs, salts and enzymes, without compromising the yield of target DNA fragments. As shown in Figure 3, MiniEnrich Purification Beads more efficiently removed excess adapter dimers (120bp) while preserving the ligated cfDNA in high yield compared to the market-leading product. Figure 4 shows that MiniEnrich Purification Beads removed short DNA fragments (<150 bp) and preserved long fragments (>150 bp) more efficiently in high yields compared to the leading products in the market.
Figure 3. Highly efficient removal of adaptor-dimer by MiniEnrich Purification Beads for cfDNA library preparation. cfDNA isolated from plasma was processed with DNA Library Prep Kit for library preparation. The purification for adaptor-ligation step and final PCR product was performed using MiniEnrich Purification Beads (blue) or a magnetic beads-based market-leading product (red).
Figure 4. Highly efficient removal of fragments (<150 bp) by MiniEnrich Purification Beads for PCR. dsDNA step ladder (20-1000 bp) in TE buffer was treated with MiniEnrich Purification Beads (blue) or a magnetic beads-based market-leading product (red).
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