Dynabeads Streptavidin Products

Dynabeads products have been used around the world in hundreds of thousands of experiments, cited in over 30,000 publications, and on countless lab shelves. Dynabeads streptavidin is used in the purification of cells, isolation of proteins, nucleic acid capture, mRNA synthesis, and NGS workflows.

Target enrichment for NGS

mRNA synthesis by in vitro transcription (IVT)

Protein and cell capture

Target sequence enrichment for NGS using Dynabeads streptavidin

Next-generation sequencing (NGS) starts with nucleic acid isolation

The first step in next-generation sequencing (NGS) is nucleic acid isolation for library preparation. The four key steps for next-generation sequencing generally include library preparation, followed by clonal amplification, sequencing of the library, and finally data analysis.

Next-generation sequencing (NGS) as a high-throughput, massive parallel sequencing technology, enables the sequencing of DNA and RNA for studying genetic variation associated with diseases and other biological processes. Applications include whole genome sequencing, deep sequence of target regions, and identification of new pathogens to further advance infectious disease and microbial research.

NGS has revolutionized genetic analysis and enabled new applications in genomic and clinical research, reproductive health, and environmental, agricultural, and forensic science.

Target enrichment by hybridization capture for NGS

Target enrichment by hybridization allows capture and therefore sufficient coverage of genomic regions from degraded sample types whether using DNA, RNA or circulating cell-free DNA from blood.

Dynabeads Streptavidin for Target Enrichment is based on the solid surface of the magnetic beads. Hybridization capture uses synthesized biotinylated oligonucleotide probes (baits) that are complementary to the genetic sequence of interest. The biotinylated probes immobilize the oligonucleotide onto the bead surface by binding with 1 μm in diameter streptavidin-coated beads. The isolated and purified target regions are subsequently amplified and prepared for sequencing.

Figure 1. Target enrichment in the NGS workflow

Figure 2. Hybridization capture with streptavidin-coated beads

Bead-based target enrichment solution for NGS

Dynabeads Streptavidin for Target Enrichment provides the following advantages:

High purity—helps minimize non-specific binding
High reproducibility—achieve consistent results and can help reduce the risk of failure
High sensitivity—secure successful NGS workflow
Automation – enables high-throughput enrichment

Streptavidin-coated Dynabeads products are among the most published magnetic beads in the NGS workflow and are recommended by some of the largest NGS solution suppliers.

Performance of Dynabeads Streptavidin for Target Enrichment in a sequencing workflow

The measured concentration of final libraries [nM] for Dynabeads Streptavidin for Target Enrichment (red bar), a positive control and streptavidin magnetic beads from 4 other vendors is shown (Figure 3). All samples were prepared in triplicates (n=3). The concentration of final libraries was calculated based on the concentration of the library fragments and the size distribution. For downstream exome sequencing, the acceptance criteria was set to 2.5 nM.

Figure 3. Concentration of final libraries

The sequencing coverage for Dynabeads Streptavidin for Target Enrichment (Figure 4, red bar), a positive control and streptavidin magnetic beads from the 2 vendors that passed the target enrichment concentration criteria outlined in figure 3. The mean coverage is expressed as an average of the triplicates, all samples were prepared in triplicates (n=3). The error bar is the standard deviation. Using Dynabeads Streptavidin for Target Enrichment gave the deepest coverage (most reads from which to build a consensus and the greatest accuracy).

Figure 4. Mean coverage

The % of the reference sequence covered vs the coverage depth for Dynabeads Streptavidin for Target Enrichment (Figure 5, red bars), a positive control and streptavidin magnetic beads from the 2 vendors that passed the target enrichment concentration criteria outlined in figure 3. For Dynabeads Streptavidin for Target Enrichment at 60x, 97.53% of the reference is covered with a minimum of 60 reads - this performance of the Dynabeads Streptavidin for Target Enrichment is particularly important for clinical applications and identification of rare variants where a deep coverage (e.g., 60x) is essential.

Figure 5. Average depth of coverage

Dynabeads streptavidin for mRNA synthesis

The success of mRNA vaccines in fighting SARS-CoV-2 and growing occurrences of chronic and infectious diseases have brought the world into a new era of vaccine development.

Designed for simple and scalable mRNA synthesis, Dynabeads Streptavidin for In Vitro Transcription is optimized for magnetic separation in a research setting.

Product benefits:

Reusability—reuse the DNA template at least 6 times to minimize plasmid preparation
Flexibility—choose synthetic or plasmid DNA template for mRNA IVT for greater flexibility of mRNA design
Automation—enables high-throughput synthesis and purification of many samples simultaneously

Figure 6. mRNA synthesis by in vitro transcription (IVT)

Dynabeads streptavidin for protein and cell capture

Order now

Benefits of Dynabeads streptavidin products

Absolute reproducibility
Low background binding
High sensitivity
Easily automated
No centrifugation, precipitation, or filtration—all you need is a magnet
Robust and gentle, with optimal binding kinetics
Few handling steps, no sample dilution, minimal sample loss

Absolute reproducibility

All Dynabeads products are produced with full control of parameters such as bead size, surface area, iron content, and magnetic mobility. The absence of excess physically adsorbed streptavidin helps ensure negligible leakage and secures a minimal batch-to-batch variation. The uniform characteristics and unique reproducibility within (CV <3%) and between batches helps reduce costs associated with quality control testing (Figure 7). Whether for your research project or for IVD testing activities, you can rely on the consistent performance of Dynabeads products.

Figure 7. Monosized superparamagnetic Dynabeads magnetic beads. Each bead has an even dispersion of magnetic material, encased within a thin polymer shell. This provides a specific and defined surface for binding your ligand. The true uniformity of all beads within each batch (typical CV <3%) provides consistent physical and chemical properties. Unique batch-to-batch reproducibility (typical CV <5%) enables reproducibility and quality of results.

Fast and flexible

Dynabeads streptavidin enables instant and efficient capture of biotinylated molecules via rapid liquid-phase kinetics. This increases speed and sensitivity compared to filters and plate-based approaches (Figure 8). Dynabeads products are truly spherical and have a large surface area per unit volume. This enables a high and constant binding capacity.

Figure 8. Dynabeads streptavidin binding kinetics are superior to traditional microtiter plates. The graph shows % binding of tumor necrosis factor (TNF) to immobilized antibody as a function of time. Courtesy of Dr. N-B Liabakk, Norwegian University of Science and Technology, Trondheim, Norway.

Robust and gentle

Dynabeads streptavidin products feature excellent mechanical and chemical stability. No iron leakage. No inhibition of enzyme activity. The monolayer of recombinant streptavidin helps ensure the vast majority of biotin-binding sites are left sterically available for binding. The technology is also very gentle, allowing isolation of proteins as well as large or unstable complexes. The native state of proteins is preserved, and fragile cells remain viable. Flexible volumes may be used, enabling isolation of low-abundance molecules. A high signal-to-noise ratio also contributes to increased sensitivity.

Easy handling—manual or automated

Magnetic separation is surprisingly easy. No tedious centrifugation, precipitation, filtration, or columns. Magnetic handling enables easy washing, separation, and concentration of your target. Excellent dispersion abilities and the lack of magnetic remanence make Dynabeads streptavidin products ideal for manual as well as automated protocols, including microfluidic systems. Depending on your specific application and target molecule, a direct or indirect capture method is applied.

How capture of molecules and cells with streptavidin beads works

When used in combination with a biotinylated probe / ligand, any target molecule can be captured on the streptavidin-coupled Dynabeads, isolated and further manipulated.

Direct or indirect capture?

Depending on your target molecule and the specific application, the direct or indirect capture method can be applied.

For some applications, using a pre-coupled ligand for direct capture allows you to reuse the Dynabeads and thus further reduce sample preparation costs.

An indirect approach can be of benefit when the concentration of your target is low, the specific affinity is weak or the binding kinetics is slow. In the indirect approach, the probe/ligand is allowed to bind to the target in suspension prior to addition of the beads.

A monolayer of streptavidin is covalently coupled to the Dynabeads, helping to ensure negligible leakage that could otherwise disturb your assay.

With streptavidin beads and the ability to work with the KingFisher instrument allows for no centrifugation steps or columns.

The Dynabeads magnetic beads enable higher-throughput applications, for which samples can be processed in 24- or 96-well plates on the KingFisher family of instruments.

To download streptavidin protocols for yourself visit out library at thermofisher.com/kingfisherprotocols and easily customize them using BindIt Software.

Also to see how the KingFisher and Dynabeads are used in the app note Mutation detection sensitivity in matched FFPE tissue and liquid biopsy samples.

Features, benefits, and applications