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MiniEnrich Carboxyl Beads (Size Selection & Purification)

Next-generation purification, size selection, and long-read size selection 

For research use only. Not for use in diagnostic procedures.

Overview, Apostle MiniEnrich Carboxyl Beads for Size Selection and Purification

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


Apostle MiniEnrich Size Selection BeadsA190606
Protocol
Apostle MiniEnrich Purification Beads
A190607
Protocol

Publication

Apostle Inc’s MiniEnrich Technology is Published at Royal Society of Chemistry’s Analyst.

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

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.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. 

Apostle MiniEnrich Carboxyl Beads offers strong magnetic response

Apostle MiniEnrichTM Carboxyl Beads are pelleted against the magnet within 25 seconds, while the market leading product takes 2 minutes and 40 seconds.


Apostle MiniEnrich Size Selection Beads

Designed for precise size selection for NGS


Introduction

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.


Performance Evaluation

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).

Exhibit 1. Less DNA residue results sharp peak with good resolution and high yield.

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.

Exhibit 2. Adjust beads to sample ratio for customized size selection.

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.

Exhibit 3. Size Selection for long fragments for long-read NGS and other applications.

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.

Apostle MiniEnrich Purification Beads

Designed for better, easier and specific removal of non-target fragments for NGS and PCR workflows


Introduction

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.


Performance Evaluation

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).

Exhibit 4. More efficient removal of fragments less than 150 bp for PCR purification.

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.

Exhibit 5. More efficient adaptor-dimer removal than competitors for cfDNA library preparation.

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.

Exhibit 6. Efficient removal of adaptor and adaptor-dimers for gDNA library preparation.

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.