Auto-Mag® HMW Size Select

Auto-Mag® HMW Size Select  is a novel magnetic bead-based reagent designed for efficient and tunable removal of short DNA fragments while simultaneously enriching high molecular weight (HMW) DNA. By adjusting the reagent-to-sample ratio, users can rapidly deplete fragments smaller than 5 kb, 10 kb, 20 kb, or 30 kb, enabling precise enrichment and recovery of target HMW DNA.

Designed to meet the stringent requirements of third-generation long-read sequencing platforms—such as PacBio SMRT and Oxford Nanopore—Auto-Mag® HMW Size Select offers key advantages, including tunable control over fragment size selection, simplified workflows, and compatibility with automated systems. It serves as a cost-effective and user-friendly alternative to other HMW size selection reagents (e.g., AMPure PB, or SRE-XS, SRE, and SRE-XL) for long-read sequencing workflows.

The core objective of Auto-Mag® HMW Size Select is to provide long-read sequencing laboratories across research, clinical, industrial, and public health sectors with greater control over the size selection of HMW DNA fragments through a tunable reagent and an automation-ready solution.

Why Choose Auto-Mag® HMW Size Select?

• Tunable Size Cutoff and Efficient Short-Fragment Depletion
  Selectively eliminates short DNA fragments and unwanted components while enriching long DNA, with flexible size cutoffs (>5kb, >10kb, >20kb or >30kb or longer )
• Preservation of Ultra-Long DNA Fragments
  Enriches long DNA while maintaining representation of ultra-long fragments (e.g., >100 kb)
• Broad Sample Compatibility
  Applicable to HMW genomic DNA, sheared or fragmented DNA, library samples, and even partially degraded gDNA samples
• High Recovery Efficiency
  Delivers up to 90% recovery, (application-dependent)
• Rapid and Flexible Protocol
  ~30-minute workflow with a flexible input DNA concentration range of 10–150 ng/µL.
• Enhanced Sequencing Performance
  Improves mean read length for long-read sequencing applications
• Versatile Workflow Integration
  Supports diverse sample types and tunable size cutoffs (5 kb–30 kb) to fit various library preparation workflows and sequencing platforms
• 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.