MiniEnrich Carboxyl Beads (Size Selection & Purification)

Apostle’s MiniEnrich Technology is published at Royal Society of Chemistry’s Analyst and is selected as a cover feature.

• High-resolution DNA size enrichment using a magnetic nano-platform and application in non-invasive prenatal testing.  Analyst. July 2020, Cover Feature, 145, 5733-5739  (PDF)
  

Abstract

Precise DNA sizing can boost sequencing efficiency, reduce cost, improve data quality, and even allow sequencing of low-input samples, while current pervasive DNA sizing approaches are incapable of differentiating DNA fragments under 200 bp with high resolution (<20 bp). In non-invasive prenatal testing (NIPT), the size distribution of cell-free fetal DNA in maternal plasma (main peak at 143 bp) is significantly different from that of maternal cell-free DNA (main peak at 166 bp). The current pervasive workflow of NIPT and DNA sizing is unable to take advantage of this 20 bp difference, resulting in sample rejection, test inaccuracy, and restricted clinical utility. Here we report a simple, automatable, high-resolution DNA size enrichment workflow, named MiniEnrich, on a magnetic nano-platform to exploit this 20 bp size difference and to enrich fetal DNA fragments from maternal blood. Two types of magnetic nanoparticles were developed, with one able to filter high-molecular-weight DNA with high resolution and the other able to recover the remaining DNA fragments under the size threshold of interest with >95% yield. Using this method, the average fetal fraction was increased from 13% to 20% after the enrichment, as measured by plasma DNA sequencing. This approach provides a new tool for high-resolution DNA size enrichment under 200 bp, which may improve NIPT accuracy by rescuing rejected non-reportable clinical samples, and enable NIPT earlier in pregnancy. It also has the potential to improve non-invasive screening for fetal monogenic disorders, differentiate tumor-related DNA in liquid biopsy and find more applications in autoimmune disease diagnosis.

The Apostle MiniEnrich Size Selection Beads are designed for size selection of DNA fragments from a mixture of DNA with various sizes, which potentially benefits downstream assays like NGS and other molecular biology workflows. 

The Apostle MiniEnrich Purification Beads are designed for purification and clean-up of DNA fragments from the contaminants in NGS and molecular biology workflows.

Features:

• Novel magnetic nanoparticles structure and proprietary surface chemistry
• Compatible with current workflows
• Enhanced performance for specific removal of non-target fragments
• Significantly improved magnetic response for less pelleting time and less beads carry-over

The Apostle MiniEnrich Size Selection Beads are designed for size selection of DNA fragments from a mixture of DNA with various sizes, which potentially benefits downstream assays like NGS and other molecular biology workflows. It can be used on samples before or after DNA fragmentation, ligation, or library amplification during NGS library preparation workflow. With proprietary Apostle MiniEnrichTM technology, the kit is featured for customized cut-off size, efficient removal of non-target fragments and recovery of target DNA fragments.

Apostle MiniEnrich Size Selection Beads is designed to precisely select DNA based on its size. It offers less DNA residue of non-target fragments, and selects DNA fragments in narrower size range, resulting sharp peak with good resolution and high yield for NGS workflows (Exhibit 1, 2, and 3).

dsDNA step ladder (50-3000 bp) in a TE buffer (red) was treated with Apostle MiniEnrichTM Size Selection Beads for left-side size selection (blue) or a magnetic beads-based market-leading product (green). Comparing to market-leading product, Apostle MiniEnrich Size Selection Beads offers less DNA residue of non-target fragments (>500 bp), while preserves fragments of interest (<500 bp) with high yield. Less DNA residue of non-target fragments results narrower size selection range, and sharp peak with good resolution and high yield.

gDNA from Hela cells was fragmented by NEBNext® dsDNA Fragmentase® (red) and Apostle MiniEnrich Size Selection Beads was used to select DNA fragments of interest. By adjusting the beads to sample ratio, the cut-off can be achieved with good yield and resolution.

The Apostle MiniEnrich Purification Beads are designed for purification and clean-up of DNA fragments from the contaminants in NGS and molecular biology workflows. It can be used on samples after DNA isolation, fragmentation, PCR amplification, cloning, library preparation, etc. With proprietary Apostle MiniEnrich technology, the kit is featured for its more efficient removal of contaminants and recovery of DNA fragments of interest than current market-leading products.

Apostle MiniEnrich Purification Beads is designed to efficiently removes small fragments like primer, primer-dimer, adaptor, and adaptor-dimer, as well as other contaminates like dNTPs, salts and enzymes, without compromising the yield of DNA fragments of interest. The more efficient removal of short fragments for PCR clean-up in library preparation work will improve sequencing efficiency and reduce cost (Exhibit 4, 5, and 6).

dsDNA step ladder (50-3000 bp) in a TE buffer (blue) was treated with Apostle MiniEnrich Size Selection Beads for right-side size selection (red). Comparing with DNA input (blue), Apostle MiniEnrich Size Selection Beads selects long DNA fragments (>1000 bp) from short fragments with good yield and resolution, which expands size selection to long-read sequencing, gaining more insights of samples.

dsDNA step ladder (20-1000 bp) in a TE buffer was treated with Apostle MiniEnrich Purification Beads (blue) or a magnetic beads-based market-leading product (red). Apostle MiniEnrich Purification Beads provides more efficient removal of short fragments (<150 bp), while preserves long fragments (>150 bp) with high yield. This data demonstrates that Apostle MiniEnrich Purification Beads can be used to remove excessive primers (20-30 bp), primer-dimers (40-60 bp), adaptors (50-60 bp), and adaptor-dimers (100-120bp), without compromising the yield of fragments of interest during molecular biology and NGS workflow.

cfDNA isolated from plasma was processed with NEBNext® UltraTM II DNA Library Prep Kit for library preparation. The purification for adaptor-ligation step and final PCR product was performed using Apostle MiniEnrich Purification Beads (blue) or a magnetic beads-based market-leading product (red). Comparing to the market-leading product, Apostle MiniEnrich Purification Beads provides more efficient removal of excessive adaptor-dimers (120bp), while preserves the ligated cfDNA with high yield.

Fragmented gDNA was processed with NEBNext® Ultra II DNA Library Prep Kit for library preparation. The purification for adaptor-ligation step and final PCR product was performed using Apostle MiniEnrich Purification Beads (red). Compared with before cleaning up (blue), Apostle MiniEnrich Purification Beads provides efficient removal of excessive adaptors (60 bp) and adaptor-dimers (120bp),while preserves the ligated gDNA with high yield.

High-resolution DNA size enrichment using a magnetic nano-platform and application in non-invasive prenatal testing.  

Zhang et al. Analyst.  July 2020, 145, 5733-5739  (PDF)

Precise DNA sizing can boost sequencing efficiency, reduce cost, improve data quality, and even allow sequencing of low-input samples, while current pervasive DNA sizing approaches are incapable of differentiating DNA fragments under 200 bp with high resolution (<20 bp). In non-invasive prenatal testing (NIPT), the size distribution of cell-free fetal DNA in maternal plasma (main peak at 143 bp) is significantly different from that of maternal cell-free DNA (main peak at 166 bp). The current pervasive workflow of NIPT and DNA sizing is unable to take advantage of this 20 bp difference, resulting in sample rejection, test inaccuracy, and restricted clinical utility. Here we report a simple, automatable, high-resolution DNA size enrichment workflow, named MiniEnrich, on a magnetic nano-platform to exploit this 20 bp size difference and to enrich fetal DNA fragments from maternal blood. Two types of magnetic nanoparticles were developed, with one able to filter high-molecular-weight DNA with high resolution and the other able to recover the remaining DNA fragments under the size threshold of interest with >95% yield. Using this method, the average fetal fraction was increased from 13% to 20% after the enrichment, as measured by plasma DNA sequencing. This approach provides a new tool for high-resolution DNA size enrichment under 200 bp, which may improve NIPT accuracy by rescuing rejected non-reportable clinical samples, and enable NIPT earlier in pregnancy. It also has the potential to improve non-invasive screening for fetal monogenic disorders, differentiate tumor-related DNA in liquid biopsy and find more applications in autoimmune disease diagnosis.