Sequence Specific DNA Capture with Streptavidin Nanobeads

Citations

1. Structural and mechanistic basis of mammalian Nudt12 RNA deNADding
2. 5′-end NAD+ cap in human cells promotes RNA decay through DXO-mediated deNADding
3. Structural and biochemical studies define Nudt12 as a new class of RNA deNADding enzyme in mammalian cells

Sequence Specific Capture

MagVigen™ magnetic nanoparticles are ideal for DNA purification with high magnetic response and superior biocompatibility, specifically tailored for the best applications in magnetic enrichment and purification, magnetofection, magnetic manipulation, magnetic sensing, and magnetic resonance imaging.

They feature efficient recovery of double-stranded and single-stranded DNA. DNA is captured by MagVigen™ magnetic nanoparticles following a short incubation. The generated nanoparticle-oligo complex can be separated from the rest of the sample by a magnet. The retained genomic material can be retrieved from the magnetic nanoparticles using an elution buffer.

DNA capture with Streptavidin nanobeads

Figure 1. Streptavidin DNA capture Scheme

Workflow

The workflow usually comprises of steps as below.

Figure 2. Streptavidin DNA capture workflow

1. Mix: Mix biotinylated probes with DNA sample.
2. Hybridization: Biotinylated probes hybridize with the desired target DNA sample.
3. Bead Capture: MagVigen™ Streptavidin beads capture biotinylated probes and the desired target DNA sample.
4. Wash: The beads respond to a magnetic force (by use of a magnet), allowing bound material to be rapidly and efficiently separated from the rest of the sample. After unbound materials are removed by aspiration, the nanoparticle-bound targets are washed by using the magnet.
5. Amplification: The captured target is amplified for downstream application, such as sequencing or diagnostics.

Applications

MagVigen™ – Streptavidin magnetic nanoparticle beads enable convenient capture of specific DNA sequence from biological samples, such as tissue lysate, whole blood and plasma samples. Captured DNA can be used in downstream applications such as NGS and clinical diagnosis.

Figure 3. sequence specific DNA capture from human blood using MagVigen™ – Streptavidin magnetic nanoparticle beads and biotin-CD19-targeted DNA probes.

MagVigen™ magnetic nanoparticle beads have smaller nanoparticle size, hence higher surface area and higher binding capacity. Smaller quantity of magnetic beads solid material is needed to achieve same capture capacity of targets compared to other magnetic beads on market. As shown in the following figure, much less MagVigen™ – streptavidin magnetic nanoparticle beads are needed when compared to conventional brand name magnetic beads – streptavidin conjugates for sequence specific DNA capture. The smaller pellet size allows less buffer volume for elution, providing a higher concentration of target molecule solution for more sensitive downstream applications, such as NGS or DNA diagnosis.

The smaller nanoparticle size, higher binding capacity, and unique surface chemistry prepared using NVIGEN’s proprietary technology make our MagVigen™ magnetic nanoparticle beads ideal for molecular and cellular purification and enrichment from complex biological samples. Shown in the following figure is for sequence specific DNA capture from fresh human whole blood samples using streptavidin conjugated magnetic beads and biotin-DNA probe. The conventional magnetic beads show severe aggregation. MagVigen™ magnetic beads enable a much cleaner magnetic capture result with much smaller pellet size and negligible aggregation for DNA extraction from whole blood samples.

Figure 4. Left side using Company A XP beads. Right side using MagVigen™ – Streptavidin nanobeads. We can see clearer solution and less beads are needed and

Sequence specific DNA capture from whole blood samples.

• Capture specific DNA molecules directly from sample solutions
• Compatible with downstream applications (NGS, clinical diagnostics)
• Smaller beads -> higher binding capacity -> less elution volume -> Higher DNA concentration
• Better for probing protein-DNA interactions

Figure 5. Comparison of poly-A loading capacity of various poly-T conjugated beads. NVIGEN oligo beads has much higher poly-A loading capacity compared to other beads due to its smaller size and higher surface area.

Figure 6. Comparison of the thermo and high pH stability of various poly-T conjugated beads. NVIGEN oligo beads have demonstrated to be extremely stable and have 100% activity after high temperature and high pH treatment

Figure 7. NVIGEN’s highly sensitive cfDNA extraction (Cat# K61003) and sequence specific target enrichment magnetic nanobeads (Cat# K61002) enable ctDNA detection at a sensitivity of a few copies of mutants. The data shows qPCR analyses of ctDNA enriched using NVIGEN’s streptavidin beads (Cat# K61002) vs. other beads (Dynabeads MyOne Streptavidin C1). For 10 and 100 copies of DNA spiking-in plasma, Dynabeads showed unreasonable, less DNA than background signal. On the contrary, NVIGEN’s K61002 nanobeads demonstrated higher sensitivity of detection down to a few mutants.

In Summary, MagVigen™ nanobeads features:

• High Yield
• Easy Workflow
• Fast Magnetic Response
• High oligo loading capacity
• Low nonspecific DNA binding
• Thermal stable (at 95°C)
• Stable at high PH

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