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Dynabeads Streptavidin Magnetic Bead Applications |
Streptavidin-biotin binding process
Streptavidin is a protein that is used extensively in molecular biology applications. Due to its exceptionally high affinity to biotin, it is among the strongest non-covalent interactions in nature. The small size of biotin makes it a popular choice for protein and cell labeling. Dynabeads streptavidin magnetic beads utilize this strong interaction to isolate cell populations, isolate target proteins, capture nucleic acids, synthesize mRNA, and prepare samples for next-generation sequencing (NGS) workflows. Learn more about the applications of using Dynabeads streptavidin beads.
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Selection guide for Dynabeads products
Dynabeads products are available for a multitude of molecular and cellular applications. Don’t know where to start? Use our easy selection guide that considers sample type, target molecule, and downstream application to provide tailored recommendations for Dynabeads products.
Dynabeads streptavidin bead selection table
Table 1. Streptavidin beads by target and application
| Target | Typical applications | Recommended products |
|---|---|---|
Nucleic acid capture |
| |
Protein isolation |
| |
Cell isolation |
|
Streptavidin beads for target sequence enrichment
NGS as a high-throughput, massive parallel sequencing technology enables the sequencing of DNA and RNA for studying genetic variations 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.
The four key steps for NGS workflow generally include library preparation, clonal amplification, library sequencing, and data analysis. Dynabeads Streptavidin for Target Enrichment is excellent for the enrichment of biotinylated target nucleic acid sequences made during the library prep as part of the NGS workflow (Figure 1).
Click image to enlarge
Figure 1. The NGS workflow. The first step for NGS is library preparation, followed by hybridization, target enrichment, PCR, and sequencing. Dynabeads Streptavidin for Target Enrichment is intended for the enrichment of the target sequences hybridized on the biotinylated probe that is immobilized to the streptavidin-coated magnetic beads (shown in red). The hybridization step can either be performed prior to the bead-based target enrichment step (indirect hybrid capture technique) or after the biotinylated probe is bound to the streptavidin beads (direct hybrid capture technique).
Bead-based target enrichment 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. The biotinylated probes (also known as bait) immobilize the oligonucleotides onto the bead surface by binding with 1 μm in diameter streptavidin beads (Figure 2). The isolated and purified target regions are subsequently amplified and prepared for sequencing.
Dynabeads Streptavidin for Target Enrichment provides the following advantages:
- High purity—helps minimize non-specific binding
- High reproducibility—helps achieve consistent results and can help reduce the risk of failure
- High sensitivity—secures successful NGS workflow
- Automation—enables high-throughput enrichment
Figure 2. Hybridization capture with streptavidin beads. Streptavidin beads immobilize the biotinylated ligand and use it as bait to capture target nucleic acid sequences.
Performance of Dynabeads Streptavidin for Target Enrichment in a sequencing workflow vs comparable products
Click image to enlarge
Figure 3. Streptavidin magnetic beads comparison: mean concentration of final libraries. We measured concentrations (nM) of final libraries for Dynabeads Streptavidin for Target Enrichment (red bar), a positive control (gray bar), and streptavidin magnetic beads from four other vendors. 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. n=3.
Click image to enlarge
Figure 4. Streptavidin magnetic beads comparison: mean coverage. Mean sequencing coverage for Dynabeads Streptavidin for Target Enrichment (red bar), a positive control (gray bar), and streptavidin magnetic beads from the two 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. Dynabeads Streptavidin for Target Enrichment gave the deepest coverage (most reads from which to build a consensus and the greatest accuracy).
Click image to enlarge
Figure 5. Streptavidin magnetic beads comparison: average depth of coverage. The % of reference sequence covered vs the coverage depth for Dynabeads Streptavidin for Target Enrichment (red bars), a positive control (gray bars), and streptavidin magnetic beads from the two 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 deep coverage (e.g., 60x) is essential.
Streptavidin beads for mRNA synthesis
Streptavidin beads can be used for mRNA synthesis by in vitro transcription (IVT), an application/workflow that can greatly accelerate the research and development of mRNA vaccines. The mRNA is synthesized using a biotinylated DNA template of choice, amplified via PCR, and immobilized to streptavidin beads (Figure 6). The immobilized template can be reused in the next IVT reaction at least six times.
Figure 6. mRNA synthesis workflow with Dynabeads Streptavidin for In Vitro Transcription. This workflow begins with the biotinylated PCR product. This mRNA template is then immobilized to the Dynabeads Streptavidin for In Vitro Transcription beads forming a bead-template complex. Using this complex, IVT can be performed up to six consecutive times. The target mRNA is then ready to be eluted from the streptavidin beads via magnetic separation and incubation with elution buffer.
Click image to enlarge
mRNA synthesis by in vitro transcription (IVT)
mRNA synthesis by IVT begins with the biotinylated template, which is made by PCR amplification of the target sequence in a plasmid construct or in a synthetic DNA construct using a biotinylated forward primer located 30–100 bps upstream of the T7-promoter and a non-biotinylated reverse primer (Figure 7). The biotinylated template is immobilized to the streptavidin beads without the need for prior purification. The streptavidin bead-bound template is used directly in IVT, then removed from the synthesized mRNA by magnetic separation. The isolated and purified target regions are subsequently amplified and prepared for sequencing.
Dynabeads Streptavidin for In Vitro Transcription is designed for simple and scalable mRNA synthesis. Product benefits include:
- Reusability—reuse the DNA template at least six times to minimize plasmid preparation and reduce hands-on time
- 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 7. mRNA synthesis by IVT using Dynabeads Streptavidin for In Vitro Transcription. The biotinylated DNA template is immobilized to the streptavidin magnetic beads and contains an upstream linker region, T7 promoter to facilitate binding of the T7 RNA polymerase, and an mRNA coding region. mRNA synthesis can be done up to six times using the same DNA template.
Click image to enlarge
Streptavidin beads for protein and cell capture
When used in combination with a biotinylated probe/ligand, any target molecule can be captured on the Dynabeads streptavidin magnetic beads, isolated and then further manipulated. Depending on your target molecule and downstream assay, a variety of products are available for protein and cell capture using streptavidin magnetic beads. View Table 2 below to determine which product meets your specific research needs.
Table 2. Streptavidin magnetic beads for direct and indirect isolation
| Recommended products | Dynabeads M-280 Streptavidin | Dynabeads MyOne Streptavidin T1 | Dynabeads Biotin Binder | CELLection Biotin Binder Kit | Dynabeads FlowComp Flexi Kit |
|---|---|---|---|---|---|
| Description |
|
|
|
|
|
| Capacity |
|
| Processes 2 x 109 PBMCs or 200 mL whole blood | Processes 2 x 109 PBMCs or 200 mL whole blood | Processes 2 x 109 MNCs or 80 mL whole blood/buffy coat |
| Ideal applications |
|
|
|
|
|
Direct and indirect capture of molecules and cells with streptavidin beads
Click image to enlarge
Depending on your target molecule and the specific application, the direct or indirect capture method can be applied using streptavidin magnetic beads (Figure 8).
For some applications, using a pre-coupled ligand in direct capture allows you to reuse the magnetic beads and thus further reduce sample preparation costs.
The indirect capture 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 indirect capture, 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 magnetic beads, helping to reduce leakage that could otherwise disturb your assay.
Figure 8. Direct and indirect capture of molecules and cells with streptavidin magnetic beads. Direct capture uses a pre-coupled ligand that is added to the sample, incubated, then eluted via magnetic separation. Indirect capture begins with incubation of the biotinylated probe/ligand to the sample, then the streptavidin magnetic beads are added and incubated for some time, followed by elution off the magnetic bead by magnetic separation.
Order Dynabeads streptavidin beads for protein and cell capture now
Streptavidin beads for target sequence enrichment
NGS as a high-throughput, massive parallel sequencing technology enables the sequencing of DNA and RNA for studying genetic variations 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.
The four key steps for NGS workflow generally include library preparation, clonal amplification, library sequencing, and data analysis. Dynabeads Streptavidin for Target Enrichment is excellent for the enrichment of biotinylated target nucleic acid sequences made during the library prep as part of the NGS workflow (Figure 1).
Click image to enlarge
Figure 1. The NGS workflow. The first step for NGS is library preparation, followed by hybridization, target enrichment, PCR, and sequencing. Dynabeads Streptavidin for Target Enrichment is intended for the enrichment of the target sequences hybridized on the biotinylated probe that is immobilized to the streptavidin-coated magnetic beads (shown in red). The hybridization step can either be performed prior to the bead-based target enrichment step (indirect hybrid capture technique) or after the biotinylated probe is bound to the streptavidin beads (direct hybrid capture technique).
Bead-based target enrichment 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. The biotinylated probes (also known as bait) immobilize the oligonucleotides onto the bead surface by binding with 1 μm in diameter streptavidin beads (Figure 2). The isolated and purified target regions are subsequently amplified and prepared for sequencing.
Dynabeads Streptavidin for Target Enrichment provides the following advantages:
- High purity—helps minimize non-specific binding
- High reproducibility—helps achieve consistent results and can help reduce the risk of failure
- High sensitivity—secures successful NGS workflow
- Automation—enables high-throughput enrichment
Figure 2. Hybridization capture with streptavidin beads. Streptavidin beads immobilize the biotinylated ligand and use it as bait to capture target nucleic acid sequences.
Performance of Dynabeads Streptavidin for Target Enrichment in a sequencing workflow vs comparable products
Click image to enlarge
Figure 3. Streptavidin magnetic beads comparison: mean concentration of final libraries. We measured concentrations (nM) of final libraries for Dynabeads Streptavidin for Target Enrichment (red bar), a positive control (gray bar), and streptavidin magnetic beads from four other vendors. 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. n=3.
Click image to enlarge
Figure 4. Streptavidin magnetic beads comparison: mean coverage. Mean sequencing coverage for Dynabeads Streptavidin for Target Enrichment (red bar), a positive control (gray bar), and streptavidin magnetic beads from the two 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. Dynabeads Streptavidin for Target Enrichment gave the deepest coverage (most reads from which to build a consensus and the greatest accuracy).
Click image to enlarge
Figure 5. Streptavidin magnetic beads comparison: average depth of coverage. The % of reference sequence covered vs the coverage depth for Dynabeads Streptavidin for Target Enrichment (red bars), a positive control (gray bars), and streptavidin magnetic beads from the two 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 deep coverage (e.g., 60x) is essential.
Streptavidin beads for mRNA synthesis
Streptavidin beads can be used for mRNA synthesis by in vitro transcription (IVT), an application/workflow that can greatly accelerate the research and development of mRNA vaccines. The mRNA is synthesized using a biotinylated DNA template of choice, amplified via PCR, and immobilized to streptavidin beads (Figure 6). The immobilized template can be reused in the next IVT reaction at least six times.
Figure 6. mRNA synthesis workflow with Dynabeads Streptavidin for In Vitro Transcription. This workflow begins with the biotinylated PCR product. This mRNA template is then immobilized to the Dynabeads Streptavidin for In Vitro Transcription beads forming a bead-template complex. Using this complex, IVT can be performed up to six consecutive times. The target mRNA is then ready to be eluted from the streptavidin beads via magnetic separation and incubation with elution buffer.
Click image to enlarge
mRNA synthesis by in vitro transcription (IVT)
mRNA synthesis by IVT begins with the biotinylated template, which is made by PCR amplification of the target sequence in a plasmid construct or in a synthetic DNA construct using a biotinylated forward primer located 30–100 bps upstream of the T7-promoter and a non-biotinylated reverse primer (Figure 7). The biotinylated template is immobilized to the streptavidin beads without the need for prior purification. The streptavidin bead-bound template is used directly in IVT, then removed from the synthesized mRNA by magnetic separation. The isolated and purified target regions are subsequently amplified and prepared for sequencing.
Dynabeads Streptavidin for In Vitro Transcription is designed for simple and scalable mRNA synthesis. Product benefits include:
- Reusability—reuse the DNA template at least six times to minimize plasmid preparation and reduce hands-on time
- 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 7. mRNA synthesis by IVT using Dynabeads Streptavidin for In Vitro Transcription. The biotinylated DNA template is immobilized to the streptavidin magnetic beads and contains an upstream linker region, T7 promoter to facilitate binding of the T7 RNA polymerase, and an mRNA coding region. mRNA synthesis can be done up to six times using the same DNA template.
Click image to enlarge
Streptavidin beads for protein and cell capture
When used in combination with a biotinylated probe/ligand, any target molecule can be captured on the Dynabeads streptavidin magnetic beads, isolated and then further manipulated. Depending on your target molecule and downstream assay, a variety of products are available for protein and cell capture using streptavidin magnetic beads. View Table 2 below to determine which product meets your specific research needs.
Table 2. Streptavidin magnetic beads for direct and indirect isolation
| Recommended products | Dynabeads M-280 Streptavidin | Dynabeads MyOne Streptavidin T1 | Dynabeads Biotin Binder | CELLection Biotin Binder Kit | Dynabeads FlowComp Flexi Kit |
|---|---|---|---|---|---|
| Description |
|
|
|
|
|
| Capacity |
|
| Processes 2 x 109 PBMCs or 200 mL whole blood | Processes 2 x 109 PBMCs or 200 mL whole blood | Processes 2 x 109 MNCs or 80 mL whole blood/buffy coat |
| Ideal applications |
|
|
|
|
|
Direct and indirect capture of molecules and cells with streptavidin beads
Click image to enlarge
Depending on your target molecule and the specific application, the direct or indirect capture method can be applied using streptavidin magnetic beads (Figure 8).
For some applications, using a pre-coupled ligand in direct capture allows you to reuse the magnetic beads and thus further reduce sample preparation costs.
The indirect capture 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 indirect capture, 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 magnetic beads, helping to reduce leakage that could otherwise disturb your assay.
Figure 8. Direct and indirect capture of molecules and cells with streptavidin magnetic beads. Direct capture uses a pre-coupled ligand that is added to the sample, incubated, then eluted via magnetic separation. Indirect capture begins with incubation of the biotinylated probe/ligand to the sample, then the streptavidin magnetic beads are added and incubated for some time, followed by elution off the magnetic bead by magnetic separation.
Order Dynabeads streptavidin beads for protein and cell capture now
Dynabeads streptavidin bead FAQs
Here are some frequently asked questions regarding the use of Dynabeads streptavidin magnetic beads.
How do you elute DNA from streptavidin beads?
A: Unless derivative forms of biotin or modified streptavidin have been adopted for your experiment, requiring a specific form and normally gentle way to dissociate biotin from streptavidin, often very harsh methods are required to dissociate the biotin from streptavidin which will denature the streptavidin. A couple of these methods are discussed below.
Biotinylated nucleic acids:
To dissociate biotinylated nucleic acids from streptavidin-coupled Dynabeads, incubate the beads in 95% formamide + 10 mM EDTA, pH 8.2 for 5 minutes at 65°C or for 2 minutes at 90°C. Pull the beads to the tube wall with the magnet and remove the supernatant containing the biotinylated nucleic acid from the tube.
Biotinylated proteins:
For biotinylated proteins, boil the beads in 0.1% SDS or SDS-PHAGE buffer for 3 min.
A: For most applications involving dissociation of biotinylated molecules from streptavidin, it is not possible to reuse the beads. The streptavidin-biotin bond is one of the strongest biological bonds known, and the conditions necessary to break this bond also destroy the streptavidin. However, if the Dynabeads streptavidin beads have been used in applications such as isolation of DNA binding proteins and release of proteins from DNA is done by gentle methods like using high-salt buffers that do not interfere with biotin-streptavidin interaction, the beads with the immobilized probe may be reused.
A: Use mild elution methods like buffers with high salt (>1 M NaOH) or low pH. Low pH elution buffers such as 0.1 M glycine•HCl, pH 2.5–3.0 are effective for most antibody-antigen interactions. Note that boiling in SDS will also elute the antibody.
Ordering information for streptavidin magnetic beads
Magnetic beads for PCR & NGS library prep size selection and cleanup
Need size selection and cleanup? Take your library prep to the next level with MagMAX Pure Bind Beads—cost-effective, energy-efficient, and high-performing magnetic beads.
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