DNA Sizing and Cleanup for NGS DNA Library Purification

Improve your DNA cleanup and size selection for high efficiency sequencing & diagnostics.

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Learn more about DNA clean-up what, why and how.

Product Features:

• Precise Size Range Selection
• High Yield High Cleanness
• Long bp or large fragment DNA Selection Available
• Easy Magnetic Workflow
• Reliable and Consistent

Citations:

1. Mutant Huntingtin Affects Diabetes and Alzheimer’s Markers in Human and Cell Models of Huntington’s Disease.
2. Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers
3. Discovery of Active Cis-Regulatory Elements and Transcription Factor Footprints in Nematodes Using Functional Genomics Approaches

MagVigen™ DNA Cleanup & Size Selection Kits

MagVigen™ – DNA Cleanup & Size Selection Kits allow simple and rapid isolation of DNA from a variety of crude sample materials (eg. NGS library, PCR constructs). It enables efficient recovery of DNA and efficient removal of unwanted contaminants (ex. primers, unincorporated dNTPs, and salts)

DNA library clean-up examples using Cat# k61001-Easy: MagVigen™ Easy DNA Cleanup & Size Selection Kit.

Before DNA Clean-up	After DNA Clean-up

Figure 1. MagVigen™ Easy DNA Cleanup & Size Selection Kit (K61001-Easy) outperforms conventional brand products for strongly contanminated NGS DNA Library sample (adapter dimer ratio 224%). After clean-up, adapter dimer over library is less than 3% using MagVigen™ (passes quality control (QC)) vs. more than 6% using AmPure XP (fails QC).

Before DNA Clean-up	After NVIGEN K61001-Easy DNA Clean-up
Tested by Agilent 2100 12000 Assay	Tested by Agilent 2100 High Sensitivity Assay

Figure 2. MagVigen™ Easy DNA Cleanup & Size Selection Kit (K61001-Easy) outperforms conventional brand products for significantly contanminated NGS DNA Library sample (adapter dimer ratio 186%). After clean-up, adapter dimer over library reduced to 2.3%.

Before DNA Clean-up	After DNA Clean-up

Figure 3. MagVigen™ Easy DNA Cleanup & Size Selection Kit (K61001-Easy) also works better for medium contanmination NGS DNA Library sample (adapter dimer ratio 68%). After clean-up, adapter dimer over library is 0.45% using MagVigen™ vs. 1.2% using AmPure XP.

Before DNA Clean-up	After DNA Clean-up

Figure 4. MagVigen™ Easy DNA Cleanup & Size Selection Kit (K61001-Easy) still works better for log contanmination NGS DNA Library sample (adapter dimer ratio 20%). After clean-up, adapter dimer undetectable using MagVigen™ vs. 0.6% using AmPure XP.

MagVigen™ DNA Size Selection magnetic nanoparticles and kits have been optimized to capture DNA with desired cutoff sizes: >50bp, >100bp, >150bp, >200bp, >300bp, >400bp, >500bp, >700bp.

Figure 5. MagVigen™ DNA Size Selection Capture DNA Fragments of Desired Size. A DNA ladder input was successfully captured for >500bp, >400bp, >300bp, >200bp.

Figure 6. shows the capture efficiency of the MagVigen™ beads for DNA fragments at a range of sizes in three different buffer conditions. A DNA ladder input was successfully captured for >150bp, >75bp, >35bp.

Figure 7. Non-hybridization based DNA capture with MagVigen™ beads can be used in a wide range of temperature conditions.

Figure 8. A use case. Customer requires 200bp cut-off and the same protocol as Company A XP beads. We can see MagVigen™ as an XP alternative: 1. At same ratio, with similar yield, MagVigen™ achieved higher fidelity. XP captured a lot 100bp. 2. From Ratio 0.8, we can see the backward trend (0.8 up) MagVigen™ has much higher sensitivity.

MagVigen™ DNA Size Range Selection Kits

MagVigen™ – DNA Cleanup & Size Selection Kits enable you to fine tune your buffer condition for DNA size range selection.

Cat# Kr61001-300/600, Kf61001-500 focus MagVigen™ provides fast and cost-effective solution to isolating DNA of desired sizes for high-quality library construction and Next-Gen Sequencing (NGS).

Figure 9. Left shows salmon genomic DNA was separated based on 2 different size range selections. 300bp<DNA<600bp can be isolated for NGS. Right shows a 500bp focused band was isolated from DNA ladder input using similar approach.

MagVigen™ DNA Easy Size Selection Kits

Figure 10. shows the sizing results by adjusting the ratios of beads volume vs. DNA sample volume. Themo Scientific GeneRuler 100 bp DNA ladder and 2% agarose gel were used.

MagVigen™ DNA Extended Long BP (500bp-3000bp) Size Selection Kits

Figure 11. NVIGEN’s MagVigen™ nanobeads (Cat# K61001-Extend) is used to size select DNA in extended DNA size range (500bp – 3000bp). 1000ng Fisher 10kb DNA ladder were size-specifically captured by adjusting volume ratio of beads to DNA volume. At 0.8 ratio, MagVigenbeads can capture DNA base pairs > 3000 bp with >80% yield, useful for longer bp DNA sequencing. Insert shows bioanalyzer result of the longer bp DNA cleanup & sizing at volume ratio of 0.8 of beads vs. DNA sample.

Two-Step DNA Cleanup For NGS Library Preparation

Figure 12. Illustration of two-step DNA Cleanup using NVIGEN’s K61001-Extend and K61001-Easy kits. Step 1 uses K61001-Extend at 0.82x to sequester longer DNA fragments. Step 2 uses K61001-Easy at 1.6x to capture DNA fragments of selected range.

MagVigen™ DNA Extend and Easy Kits For Two-Step DNA Cleanup

Figure 13. MagVigen™ K61001-Extend kit was used in the first step of DNA cleanup to capture longer fragments in standard DNA ladder (Thermo Scientific GeneRuler 100 bp DNA Ladder, DNA size ranging from 100 bp to 1,000 bp) followed by K61001—Easy kit to capture shorter DNA fragments. The adjusted bead volume ratios 0.85X was used in the first step, 1.2X in the second step. The stack bar chart shows the NVIGEN’s MagVigen™ K61001-Extend nanobeads were able to capture uptrend amount of longer DNA fragments (top orange bar) in the first step. The remaining shorter DNA fragments were then captured by K61001-Easy beads. Both products have demonstrated high efficiency and consistency with CV less than 10% across all batches. The total yield is obtained based on TECAN fluorescent plate reading to measure the fluorescent signal of the Pico green dye that intercalates dsDNA.

MagVigen™ DNA Extend and Easy Kits For Two-Step DNA With Volume Ratio Adjustment

Figure 14. Volume ratio of MagVigen K61001 kits in two-step DNA cleanup can be adjusted to suit customized need. In the first step of DNA cleanup, MagVigen™ K61001-Extend kit with beads in 1.2X volume ratio was used to capture larger DNA fragments in standard DNA ladder (Thermo Scientific GeneRuler 100 bp DNA Ladder, DNA size ranging from 100 bp to 1,000 bp), followed by K61001—Easy beads with bead volume ratio of 1.2X. The stack bar chart shows the NVIGEN’s MagVigen™ K61001-Extend nanobeads were able to capture more shorter DNA fragments (top orange bar) in the first step. The remaining DNA fragments were then captured by K61001-Easy beads. Both products have demonstrated high efficiency and consistency with CV less than 10% across all batches. The total yield was obtained using the same method as in Figure 13.

MagVigen™ K61001 Kits – Consistency and Robust in DNA Clean-up

Figure 15. MagVigen™ K61001-Easy nanobeads were used in DNA cleanup to capture 100ng standard DNA ladder (Thermo Scientific GeneRuler 100 bp DNA Ladder, DNA size ranging from 100 bp to 1,000 bp). The adjusted bead volume ratios (0.85X and 1.2X) were used in triplicate. The observed results clearly show high efficiency and consistency in these experiments (CV less than 10% across all batches). The total yield is obtained based on TECAN fluorescent plate reader to measure the fluorescent signal of the Pico green dye that intercalated dsDNA.

In Summary, MagVigen™ nanoparticles features:

• Volume Ratio or Streptavidin Based DNA Selection
• Long bp DNA (500p-3000bp) Selection Available
• Precise Size Range Selection
• High Yield
• Easy Workflow
• Fast Magnetic Response

Learn more about the basics & development of DNA Size Selection and DNA cleanup,

Learn which scientists are citing this product series on what projects.

K61001 FAQ