Auto-Mag® HMW Size Select

Auto-Mag® HMW Size Select is an innovative and truly practical reagent that utilizes advanced nanomagnetic bead technology to efficiently sort, purify, and recover high molecular weight (HMW) DNA fragments. Its user-friendly operation allows precise adjustment of the reagent-to-sample volume ratio, enabling the rapid and effective removal of short DNA fragments from HMW genomic DNA samples. This process selectively retains large DNA fragments—such as those exceeding 5 kb, 10 kb, 20 kb, or 30 kb, meeting the stringent requirements of third generation long-read sequencing platforms like PacBio SMRT and Oxford Nanopore.

Third-generation sequencing technologies demand high-quality, long-length DNA templates to ensure accurate and reliable results. However, genomic DNA samples are often contaminated with short fragments due to factors such as suboptimal sample quality or partial degradation during extraction or storage. These short fragments can compromise sequencing accuracy and performance, making their removal critical. Auto-Mag® HMW Size Select effectively addresses this issue by selective recovery of high-quality HMW DNA while removing unwanted short fragments. By enriching large DNA fragments, it enhances sample quality and improves sequencing performance, yielding longer read lengths and greater accuracy.

Auto-Mag® HMW Size Select offers exceptional adaptability, delivering optimal performance with DNA sample concentrations ranging from 10 to 150 ng/μl. Its advanced technology eliminates the need for centrifugation or filtration, simplifying workflows and enhancing efficiency. Designed with both flexibility and convenience in mind, it supports manual operation as well as integration with automated liquid handling systems. This makes it a reliable, efficient, and powerful solution for researchers seeking high-quality HMW DNA to meet the demands of high-throughput long-read sequencing workflows.

Key Features

• Innovative and Practical HMW DNA Size Selection: Magnetic bead-based solution for efficient enrichment of high molecular weight DNA
• Tunable Size Cutoff: Precise control through adjustment of the reagent-to-sample ratio
• Rapid and Efficient Recovery: Selective enrichment of HMW DNA fragments (>5kb, >10kb, >20kb or >30kb or longer ) within ~30 minutes
• Effective Removal of Short Fragments and Impurities: Eliminates small DNA fragments and unwanted reaction components
• High Recovery Yield: Up to 90% (application-dependent)
• Enhanced Sequencing Performance: Improves mean read length for long-read sequencing applications
• Centrifugation-Free Workflow: Simplifies operation and minimizes sample loss
• Automation-Ready: Compatible with liquid handling systems and high-throughput workflows
• Cost-Effective Alternative: Delivers high performance without the need for expensive instrumentation

HMW gDNA Size Selection & Cleanup Workflow

1.  Confirm the gDNA sample volume.
2.  Add appropriate volume of Auto-Mag® HMW Size Select  to the sample.
3.  Rotate the sample at room temperature for selective binding HMW DNA
4.  Separate the beads from contaminants and short DNA fragments.
5.  Wash magnetic beads with 85% ethanol.
6.  Elute size-selective HMW gDNA from magnetic beads.

Data & References

The HMW DNA size selection and cleanup

Fig 1. Selective recovery of DNA fragments across different size ranges from a 25 µL gDNA sample using varying reagent-to-sample volume ratios of Auto-Mag® HMW Size Select. The recovered HMW DNA fragments were eluted in 25 µL of elution buffer and analyzed using the Agilent TapeStation 2200.

Short DNA fragment depletion and size selection

Figure 2. Illustration of the performance of Auto-Mag® HMW Size Select Reagent in DNA size selection versus size cutoff. The input DNA was a mixture of HMW DNA spiked with a 1kb DNA Ladder (Thermo Scientific GeneRuler 1 kb Plus, #SM1331). By adding different volume ratios of Auto-Mag® HMW Size Select reagent to the sample, the unwanted short DNA fragments were effectively and controllably reduced to trace levels, while the larger DNA fragments were recovered within the desired size range. The test results were analyzed on an Agilent TapeStation 2200. Next few figures are some individual detail ratio examples.

Figure 2-1 (1.6x)                                                                Figure 2-2 (1,5x)

Figure 2-3 (1.45x)                                                              Figure 2-4 (1.35x)   

Figure 2-1, 2-2. 2-3 & 2-4 shows in more detail size selection capabilities of Auto-Mag® HMW Size Select on HMW DNA spiked with a 1kb Ladder. 

2-1: By using a 1.6x ratio of Auto-Mag® HMW Size Select to HMW DNA sample,
        >3kb DNA can be recovered while <3kb DNA fragments in length is depleted.  

2-2: By using a 1.5x ratio of Auto-Mag® HMW Size Select to HMW DNA sample,
        >5kb DNA can be recovered while <5kb DNA fragments in length is depleted.  

2-3: By using a 1.45x ratio of Auto-Mag® HMW Size Select to HMW DNA sample,
        >10kb DNA can be recovered while <10kb DNA fragments in length is depleted.  

2-4: By using a 1.35x ratio of Auto-Mag® HMW Size Select to HMW DNA sample,
        >20kb DNA can be recovered while <20kb DNA fragments in length is depleted.  

The recovery of HMW DNA size select

Figure 3. Using two MegaRaptor fragmented gDNA mixtures as input, the concentration of 3k-15kb DNA fragments was 77.4 ng/μl and the concentration of 15kb-60kb DNA fragments was 62.2 ng/μl. After using 1.4x Auto-Mag® HMW Size Select, the 3k-15kb DNA fragments were reduced to 10.9 ng/μl, while the 15kb-60kb DNA fragments were still 63.8 ng/μl, indicating that Auto-Mag® HMW Size Select can recover all DNA fragments in the selected size range. The recovery rate was over 90%.

Comparison of <10kb DNA deletion

Figure 4. Comparison of HMW DNA selection using Auto-Mag® HWM Size Select (1.45x) and AMPure PB (0.45x) according to their respective protocols on gDNA spiked with 1kb Plus DNA ladder (at 50ng/μl). Data were analyzed on an Agilent TapeStation 2200 system. Auto-Mag® HMW Size Select has better performance and accuracy in removing DNA fragments <10kb and recovering large DNA fragments in the desired size range.