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Dynabeads™ DNA DIRECT™ Universal Kit - FAQs

Dynabeads™ DNA DIRECT™ Universal Kit - FAQs

查看更多产品信息 Dynabeads™ DNA DIRECT™ Universal Kit - FAQs (63006)

54 个常见问题解答

使用Dynabeads DNA DIRECT试剂盒时，出现高PCR背景，是什么原因造成的？

高PCR背景可能是由过高的模板DNA、引物、Mg2+或dNTPs浓度所致。为解决这个问题，可以减少模板DNA、引物、酶和Mg2+的使用量，在PCR扩增前洗脱DNA，以及尝试使用热启动PCR。高背景也可能是由污染所致。应确保每次洗涤都完全去除上清液，避免残留。

我发现在使用Dynabeads DNA DIRECT试剂盒时DNA的洗脱效率不高。你们有什么建议来改善这种情况吗？

我们推荐用重悬缓冲液，水或低离子强度的缓冲液65°C孵育5分钟以上来洗脱DNA。洗脱前确保复合物被充分重悬。重悬缓冲液可预热至65°C。孵育后将管子放在磁力架上30秒，把上清移至另一干净的管子中。你可以用部分洗脱的DNA进行琼脂糖凝胶电泳来评估洗脱效率。或者你也可用Dynabeads做模板进行PCR来评估残留在磁珠上的痕量DNA。加更多预热的洗脱缓冲液对提高洗脱效率会有帮助。

我在使用你们的Dynabeads DNA DIRECT试剂盒进行PCR时，未出现任何扩增，该如何处理？

PCR可能被抑制剂抑制，或PCR循环数不足。对于抑制剂，应确保洗涤缓冲液恢复到室温后再使用，并增强加入缓冲液的力度。还应确保每一次清洗步骤中都完全去除上清液，或增加一次额外的清洗步骤。

我的Dynabeads磁珠不能很好地吸附到磁力架上，对此你们有什么建议吗？

请查看以下可能原因：

•溶液太粘稠。
•蛋白质间相互作用导致磁珠聚集。

尝试以下建议：
•延长分离时间（将管子留在磁力架上2-5分钟）。
•向裂解液中加入DNase I（约0.01 mg/mL）。
•将结合和/或清洗缓冲液中的Tween20浓度增加至约0.05%。
•向结合和/或清洗缓冲液中加入最多至20 mM 的β-巯基乙醇。

我想要分离较长的双链DNA片段，你们有什么产品可以推荐？

对于小于1 kb的生物素标记DNA，我们推荐使用Dynabeads M270链霉亲和素磁珠和MyOne C1磁珠。对于大于1kb的双链DNA分子，我们推荐Dynabeads KilobaseBINDER试剂盒。KilobaseBINDER试剂包括M-280链霉亲和素偶联的Dynabeads磁珠和一种含有专利的固定活化剂的结合液，可结合较长的生物素化DNA分子以进行分离。请点击以下链接(https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/napamisc/capture-of-biotinylated-targets/immobilisation-of-long-biotinylated-dna-fragments.html)，查看关于长的生物素化DNA片段分离的更多信息。

我能否使用Dynabeads磁珠分离单链DNA模板？

可以，Dynabeads磁珠可用于分离单链DNA。链霉亲和素Dynabeads磁珠能够以生物素化的DNA片段为靶标，通过使双链DNA变性，从而去除非生物素化链。链霉亲和素偶联的Dynabeads磁珠不会抑制任何酶活性。因此，可以在固相上直接对磁珠结合的DNA进行下一步处理。请点击以下链接(https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/napamisc/capture-of-biotinylated-targets/preparing-single-stranded-dna-templates.html)，查看关于单链DNA捕获的更多信息。

什么是磁化率？

磁化率能够衡量磁珠向磁力架迁移的速度，其大小取决于铁含量和氧化铁的特性。Dynabeads磁珠的磁化率是指质量磁化率，单位可以是cgs单位/g或m^3/kg（国际单位制）。对于亚铁磁性和铁磁性物质，质量磁化率取决于磁场强度（H），这些物质的磁化强度与H不是线性关系，而是随着场强增加而趋于饱和。因此， Dynabeads磁珠的质量磁化率是在固定条件下由标准操作程序而测定的。我们产品目录中给出的质量磁化率是国际单位制。磁化率由从高斯（cgs、emu）单位向国际单位的转换，是通过“高斯系数（emu/g或cgs/g）x 4π x 10^-3”而实现的。所得单位也被称为合理化质量磁化率，与（国际单位制）无量纲磁化率单位有所区别。通常，质量磁化率可用来衡量在非均匀磁场中影响物体的力（Fz）。测定Dynabeads磁珠的质量磁化率时，首先对样本称重，然后将样本放置于已知强度的磁场中。随后，再次称重得到样本重量（F1），并与关闭磁场时样本的重量（F0）进行对比。使用下述公式计算磁化率：K x 10^–3 = [(F1-F0) x m x 0.335 x 10^6]，K表示质量为m的样本的质量磁化率。最后，将磁化率转换为国际单位制。

我如何确定Dynabeads磁珠的偶联效率？

有多种不同的方法可以检测配体与磁珠结合，包括光密度（OD）检测、荧光标记和放射性标记。

对于OD检测，应在配体固定到磁珠上之前检测配体的OD值，并将其与包被后上清液中剩余的配体浓度进行比较。这样可以粗略检测有多少蛋白与磁珠结合。 实验方案： 1.将分光光度计设置到正确的波长。使用偶联缓冲液作为空白组。 2.检测偶联前溶液的吸光值。根据配体的加入量，可能需要进一步稀释以读取吸光值。 3.检测偶联后溶液的吸光值。也可能需要进一步稀释以读取吸光值。 4.计算偶联效率，以“蛋白质摄取量%”表示，如下所示：[(偶联前溶液的吸光值x D) – (偶联后溶液的吸光值x D)] x 100/(偶联前溶液的吸光值 x D)，D = 稀释倍数。 对于荧光标记，我们建议对配体结合量进行反向定量，即检测偶联上清液中剩余的配体量（与原始样本对比），而不是直接检测磁珠上的配体量。将标记的配体加入到磁珠中，并检测上清液中剩余多少配体（而不是结合到磁珠上的配体）。通过与开始时加入的总配体量相比，可以计算出结合到磁珠上的配体量。由于Dynabeads磁珠具有自发荧光，因此，我们不推荐直接检测与磁珠结合的配体的荧光，而是推荐这种间接方法。标记物可以是FITC/PE等。有些研究人员也成功使用了直接检测方法（采用流式细胞仪）。 在3种方法中，放射标记的灵敏度最高，但难度最大。该方法涉及到对配体的一部分进行放射性标记。在偶联前，使用示踪剂量的放射性标记的I-125，将其以一定比例与“冷”配体混合。使用闪烁（γ）计数器对磁珠进行检测，并将磁珠的cpm值与标准品对比，得到磁珠上配体的绝对量。 实验方案： 1.取出适量磁珠，并使用1 mL结合缓冲液清洗。 2.吸取适量人IgG，置于一个单独的管子中。 3.将人IgG与I-125标记的人IgG（30,000–100,000 cpm）混合。 4.使用结合缓冲液将人IgG与I-125标记的人IgG混合物稀释至100mL。 5.室温下孵育30分钟，使用闪烁计数器检测cpm值。 6.清洗磁珠（和包被层）4次，再次检测cpm值。 使用下述方程计算结合率%：（清洗后cpm值/清洗前cpm值）x100%。

Dynabeads磁珠有哪些尺寸？

Dynabeads磁珠有3种尺寸：4.5 µm （M-450）、2.8 µm （M-270/M-280）和1 µm （MyOne beads）。其中最大尺寸的磁珠非常适合细胞等较大的目标，2.8 µm磁珠推荐用于蛋白质组学和分子研究，而最小的1 µm磁珠则适用于自动化处理。

Dynabeads磁珠可使用超声处理么？

一般来说，在加入配体包被磁珠时，短时间超声是减少磁珠聚集、确保磁珠获得最佳均一性的好方法。一旦目标分子结合到磁珠，就要加倍小心了，以防结合被破坏。链霉亲和素磁珠本身能够承受超声。超声5分钟是可以的，更长时间超声的影响还未被测试。关于链霉亲和素-生物素的相互作用可否被超声破坏目前也尚无相关信息。

Dynabeads磁珠能否灭菌？

只有未包被的环氧基或甲苯磺酰基活化的磁珠可根据需要使用70%乙醇进行清洗除菌。包被的磁珠不可灭菌。

什么是Dynabeads磁珠？

Dynabeads磁珠是一种大小均一、无孔、超顺磁的、单分散的、高度交联的聚苯乙烯微球，整个磁珠由均匀分散的磁性材料构成。该磁性材料由磁赤铁矿(γ-Fe2O3)和磁铁矿(Fe3O4)的混合物组成。在Dynabeads磁珠M-280和M-450中，铁(Fe)分别占磁珠重量的12%和20%。Dynabeads磁珠表面覆盖有一层薄的聚苯乙烯外壳，将磁性材料包裹在内，可防止磁珠泄漏或在内部捕获配体。此外，该外壳也可避免目标分子直接接触铁，同时为每次实验提供特定的表面来吸附或偶联各种分子。
磁珠尺寸和形状均一，确保物理和化学性质稳定一致，进而提高实验结果的质量和可重复性。
Dynabeads磁珠分为3种不同尺寸：4.5 μm （M-450磁珠），2.8 μm （M-270/M-280磁珠）和1 μm （MyOne磁珠）。

使用Dynabeads磁珠，能否从同一样本中分离基因组DNA和mRNA？

可以从同一样本中分离出基因组DNA和mRNA，但是，我们推荐首先使用Dynabeads DNA DIRECT通用试剂盒分离DNA，以避免较大的DNA片段在mRNA分离过程中结合到磁珠上。

分离出基因组DNA后，您可使用Dynabeads mRNA DIRECT试剂盒或Dynabeads mRNA DIRECT微量试剂盒从同一的裂解液中分离mRNA（只需在裂解液中加入Dynabeads Oligo (dT)25磁珠，不要使用试剂盒中的裂解/结合缓冲液，按说明书进行后续操作）。

I am seeing high PCR background when using the Dynabeads DNA DIRECT Kit. What could be the cause of this?

High PCR background could be caused by too high a concentration of template DNA, primers, Mg2+, or dNTPs. To fix this, reduce the amount of template DNA, primers, enzyme, and Mg2+ used, elute the DNA prior to PCR amplification, and/or try performing hot-start PCR. High background can also be caused by contamination. Ensure that the supernatant is completely removed at each washing step to avoid carryover.

I am getting inefficient elution of my DNA when using the Dynabeads DNA DIRECT Kit. Do you have any suggestions to improve this?

We recommend eluting the DNA in Resuspension Buffer, water, or low ionic strength buffer by incubation at 65 degrees C for > 5 mins. The complex must be fully resuspended before elution. The elution buffer can be pre-heated to 65 degrees C. After incubation, place tube in magnetic stand for 30 secs and transfer supernatant to a clean tube. To determine the elution efficiency, you can run some of the eluted DNA on an agarose gel. Alternatively, you can perform a PCR with the Dynabeads magnetic beads to determine if there is residual DNA remaining on the beads. Using more pre-heated elution buffer would be helpful to improve the elution efficiency.

I do not see any amplification when using your Dynabeads DNA DIRECT Kit for PCR. What should I do?

PCR may be inhibited by inhibitors, or an insufficient number of PCR cycles might have been used. For inhibitors, ensure that the washing buffer is brought to room temperature for use, and add the buffer more vigorously. You can also ensure that the supernatant is completely removed at each washing step, or introduce an additional washing step.

My Dynabeads magnetic beads are not pelleting well with the magnet. Do you have any suggestions for me?

Please review the following possibilities for why your Dynabeads magnetic beads are not pelleting:

- The solution is too viscous.
- The beads have formed aggregates because of protein-protein interaction.

Try these suggestions: - Increase separation time (leave tub on magnet for 2-5 minutes)
- Add DNase I to the lysate (~0.01 mg/mL)
- Increase the Tween 20 concentration to ~0.05% of the binding and/or washing buffer.
- Add up to 20 mM beta-merecaptoethanol to the binding and/or wash buffers.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

I have a long double-stranded DNA fragment I would like to isolate. What product do you recommend?

For biotin-labeled DNA that is less than 1 kb, we recommend you use Dynabeads M270 Streptavidin (Cat. No. 65305) and MyOne C1 magnetic beads (Cat. No. 65001). We recommend our Dynabeads KilobaseBINDER Kit (Cat. No. 60101), which is designed to immobilize long (>1 kb) double-stranded DNA molecules. The KilobaseBINDER reagent consists of M-280 Streptavidin-coupled Dynabeads magnetic beads along with a patented immobilization activator in the binding solution to bind to long, biotinylated DNA molecules for isolation. Please see the following link (https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/napamisc/capture-of-biotinylated-targets/immobilisation-of-long-biotinylated-dna-fragments.html) for more information in regards to long biotinylated DNA fragment isolation.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

Can I use Dynabeads magnetic beads to isolate single-stranded DNA templates?

Yes, Dynabeads magnetic beads can be used to isolate single-stranded DNA. Streptavidin Dynabeads magnetic beads can be used to target biotinylated DNA fragments, followed by denaturation of the double-stranded DNA and removal of the non-biotinylated strand. The streptavidin-coupled Dynabeads magnetic beads will not inhibit any enzymatic activity. This enables further handling and manipulation of the bead-bound DNA directly on the solid phase. Please see the following link (https://www.thermofisher.com/us/en/home/life-science/dna-rna-purification-analysis/napamisc/capture-of-biotinylated-targets/preparing-single-stranded-dna-templates.html) for more information in regards to single-stranded DNA capture.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

What is the magnetic susceptibility for Dynabeads magnetic beads?

Magnetic susceptibility is a measure of how quickly the beads will migrate to the magnet. This will depend on the iron content and the character of the iron oxide. The magnetic susceptibility given for the Dynabeads magnetic beads is the mass susceptibility, given either as cgs units/g or m^3/kg (the latter being an SI unit). For ferri- and ferromagnetic substances, the magnetic mass susceptibility is dependent upon the magnetic field strength (H), as the magnetization of such substances is not a linear function of H but approaches a saturation value with increasing field. For that reason, the magnetic mass susceptibility of the Dynabeads magnetic beads is determined by a standardized procedure under fixed conditions. The magnetic mass susceptibility given in our catalog is thus the SI unit. Conversion from Gaussian (cgs, emu) units into SI units for magnetic mass susceptibility is achieved by multiplying the Gaussian factor (emu/g or cgs/g) by 4 pi x 10^-3. The resulting unit is also called the rationalized magnetic mass susceptibility, which should be distinguished from the (SI) dimensionless magnetic susceptibility unit. In general, magnetic mass susceptibility is a measure of the force (Fz) influencing an object positioned in a nonhomogenous magnetic field. The magnetic mass susceptibility of the Dynabeads magnetic beads is measured by weighing a sample, and then subjecting the sample to a magnetic field of known strength. The weight (F1) is then measured, and compared to the weight of the sample when the magnetic field is turned off (F0). The susceptibility is then calculated as K x 10^-3 = [(F1-F0) x m x 0.335 x 10^6], where K is the mass susceptibility of the sample of mass m. The susceptibility is then converted to SI units.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

How can I determine coupling efficiency of Dynabeads magnetic beads?

There are different methods to check binding of ligands to the beads, including optical density (OD) measurement, fluorescent labeling, and radioactive labeling.

For OD measurement, you would measure the OD of the ligand before immobilization to the beads and compare it with the ligand concentration that is left in the supernatant after coating. This gives a crude measurement of how much protein has bound to the beads.

Protocol:

1.Set spectrophotometer to the right wavelength. As a blank, use the Coupling Buffer.
2.Measure the absorbance of the Pre-Coupling Solution. A further dilution may be necessary to read the absorbance, depending upon the amount of ligand added.
3.Measure the absorbance of the Post-Coupling Solution. A dilution may be necessary to read the absorbance.
4.Calculate the coupling efficiency, expressed as the % protein uptake, as follows. [(Pre-Coupling Solution x D) - (Post-Coupling Solution x D)] x 100/(Pre-Coupling Solution x D) where D = dilution factor.

For fluorescent labeling, we suggest negatively quantifying the amount of ligand bound by measuring ligand remaining in the coupling supernatant (compared to the original sample), rather than directly measuring the ligands on the beads. Add labeled ligand to the beads, and measure how much ligand is left in the supernatant (not bound to the beads). By comparing this with the total amount added in the first place, you can then calculate how much of the ligand that has been bound to the beads. Keep in mind that the Dynabeads magnetic beads are also autofluorescent, which is why direct measuring of fluorescence of the bead-bound ligands is not recommended, but rather this indirect approach. The label could be, for example, FITC/PE. Some researchers perform a direct approach with success (using a flow cytometer).

Radioactive labeling is the most sensitive method of the three, but it is also the most difficult one. It involves radioactively labeling a portion of the ligand. We use radiolabeled I-125 in tracer amounts and mix it with "cold" ligands in a known ratio before coupling. The absolute quantities for the ligand on the beads should be obtained by measuring the beads in a scintillation (gamma) counter and comparing the cpm with a standard.

Protocol:

1.Take out an appropriate amount of beads and wash the beads in 1 mL of binding buffer.
2.Pipette out desired amount of human IgG in a separate tube.
3.Mix the human IgG with I-125-labeled human IgG (30,000 - 100,000 cpm).
4.Dilute the mixture of human IgG and I-125-labeled human IgG to 100 mL in binding buffer.
5.Incubate for 30 minutes at room temperature and measure the cpm in a scintillation counter.
6.Wash the beads (with coating) four times, and measure cpm again.
The % binding is calculated by using the equation : (cpm after washing/cpm before washing)x100%.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

What sizes do you offer for the Dynabeads magnetic beads?

Dynabeads magnetic beads come in three sizes: 4.5 µm (M-450), 2.8 µm (M-270/M-280), and 1 µm (MyOne beads). The largest of the Dynabeads magnetic beads is ideal for big targets like cells. The 2.8 µm beads are recommended for proteomics and molecular applications. The smallest of the beads, 1 µm, are ideal for automated handling.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

Can Dynabeads magnetic beads be sonicated?

In general, short sonication is a good way to reduce aggregation of the beads and ensure optimal homogenous conditions at the time of ligand addition when coating the beads. When target is bound to the beads, more care is needed, as the binding might break. The streptavidin beads themselves should tolerate sonication. We have not tested sonication for long periods, but 5 minutes is fine. We do not have information about the streptavidin-biotin interaction being broken by such treatment.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

Can Dynabeads magnetic beads be sterilized?

If desired, the uncoated epoxy or tosylactivated beads can be sterilized by washing with 70% ethanol. Coated beads cannot be sterilized.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center.

What are Dynabeads magnetic beads?

Dynabeads magnetic beads are uniform, non-porous, superparamagnetic, monodispersed and highly cross-linked polystyrene microspheres consisting of an even dispersion of magnetic material throughout the bead. The magnetic material within the Dynabeads magnetic beads consists of a mixture of maghemite (gamma-Fe2O3) and magnetite (Fe3O4). The iron content (Fe) of the beads is 12% by weight in Dynabeads magnetic beads M-280 and 20% by weight in Dynabeads magnetic beads M-450. The Dynabeads magnetic beads are coated with a thin polystyrene shell which encases the magnetic material, and prevents any leakage from the beads or trapping of ligands in the bead interior. The shell also protects the target from exposure to iron while providing a defined surface area for the adsorption or coupling of various molecules.

Uniformity of bead size and shape provides consistent physical and chemical properties. These uniform physical characteristics lead to high-quality, reproducible results.

The Dynabeads magnetic beads are available in three different sizes: 4.5 µm (M-450 beads), 2.8 µm (M-270/M-280 beads) and 1 µm (MyOne beads).

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

Can Dynabeads DNA DIRECT Universal Kit be used for isolation of bacterial DNA directly from soil?

It might be possible to isolate bacterial DNA directly from soil but soil samples are difficult to work with, as there are a lot of PCR inhibitors present. Please check scientific literature for suggested protocols.

Why are LiCl and LiDS included in Dynabeads buffers?

Lithium chloride is included in Washing Buffer A to ensure that the mRNA remains annealed to the Oligo(dT)25 on the beads while everything else is washed away. The major advantage of using LiCl instead of other chloride salts is that LiCl does not efficiently precipitate DNA, proteins, or carbohydrates and therefore reduces the risk of contamination of the final mRNA preparation with DNA and inhibitors of cDNA synthesis, PCR etc.

LiDS is an ionic detergent, similar in function to SDS. LiDS is included in the lysis buffer is to aid in the lysis of the cells and to denature proteins, and in addition it is an effective RNase inhibitor. If you don't have LiDS in the lab, it is also possible to use SDS, but you may wish to add RNAse inhibitor as well.

What is the Dynabeads DNA DIRECT Universal kit?

Dynabeads DNA DIRECT Universal Kit (Cat. No. 63006) is designed for genomic DNA isolation. This kit will not be able to isolate small DNA fragments or plasmids, the smallest DNA isolated with this kit is about 17kb.

The Dynabeads DNA DIRECT Kit does not involve any "specific capture" of DNA, but rather adsorption of DNA onto the Dynabeads magnetic beads surface. Dynabeads DNA DIRECT Universal Kits contain a Lysis and Binding buffer that facilitate the precipitation of the DNA onto the beads surface - a combination of detergents and salt result in precipitation of DNA.

Can genomic DNA and mRNA be isolated from the same sample with Dynabeads magnetic beads?

Both genomic DNA and mRNA can be isolated from the same sample, but we recommend that you isolate the DNA first using the Dynabeads DNA DIRECT Universal Kit in order to avoid large DNA fragments binding to the Oligo(dT)25 beads during the mRNA isolation procedure.

After genomic DNA is isolated, you can use the Dynabeads mRNA DIRECT Kit or Dynabeads mRNA DIRECT Micro Kit to isolate the mRNA from the same lysate (just add the Dynabeads Oligo (dT)25 magnetic beads to the lysate, don't use the lysis/binding buffers in the kit, and follow the remainder of the protocol).

If the Dynabeads DNA Direct magnetic beads do become dried, will they still work?

Vials containing Dynabeads magnetic beads should be stored upright to ensure that the beads are covered with buffer. Drying of Dynabeads magnetic beads may reduce their efficiency. If Dynabeads magnetic beads do become dried, they should be resuspended by keeping the vial in motion on a roller for up to 12 hours. This should restore the functionality of the Dynabeads magnetic beads.

How should the Dynabeads DNA Direct kit be stored?

All components of the kit should be stored at 2 to 8 degrees C. Freezing of the kit is not recommended. All components of the kit needs to be brought to room temperature before use. Dynabeads magnetic beads and any precipitated detergent should be fully resuspended.

Can the Dynabeads DNA Direct Universal Kit be used to isolate plasmid DNA?

The kit is designed for the isolation of double-stranded DNA molecules larger than 17 kb. If you have a strain of bacteria with a high copy-number of plasmids, you will co-isolate some plasmid DNA together with the bacterial genomic DNA. The process of isolating DNA with this kit is based on unspecific adsorption of DNA to the surface of these specific beads upon lysis. Due to their low size, plasmids will be lost in the supernatant during washing steps. For specific capture of plasmid DNA, use a biotinylated oligo and Streptavidin-Coupled Dynabeads magnetic beads.

Are Dynabeads DNA Direct magnetic beads reusable?

Dynabeads DNA Direct magnetic beads are not reusable. It will never be possible to remove all traces of DNA from the magnetic beads. As with used tubes and pipette tips, traces of DNA on the beads will contaminate downstream PCR on a future sample.

Can the purity of the isolated DNA be measured by an OD reading?

To use optical density measurements to determine DNA purity, the DNA will first have to be eluted from the Dynabeads magnetic beads. Ensure that there are no Dynabeads magnetic beads left in the solution, as the beads will interfere with the spectrophotometrical readings.

How should DNA isolated with Dynabeads DNA Direct kit be stored?

The DNA/Dynabeads complex may be stored for up to one week at 4 degrees C. For longer periods, DNA should be eluted and stored at -20 to -70 degrees C.

Is it necessary to elute the DNA from Dynabeads magnetic beads prior to PCR?

No, the beads do not have inhibitory effects when recommended concentrations are applied. If the DNA is to be stored prior to PCR amplification, elution is recommended.

How should the DNA/Dynabeads complex be handled?

The complex will appear gelatinous. Removal of lysate should be performed carefully to avoid loss of the DNA/Dynabeads complex, and completely to remove all contaminants. To avoid withdrawing the complex into the pipette tip when aspirating the supernatant, a stepwise removal of the supernatant is recommended. Washing buffer should be pipetted into the test tube in a single, rapid pipetting action so that the complex is swirled around in the buffer. To avoid loss of material, it is important that the complex is not broken up until the addition of the Resuspension Buffer.

Why are the Dynabeads magnetic beads supplied in a lysis buffer?

Upon addition of the lysis buffer the cells will lyse and release the DNA, which will then bind instantly to the Dynabeads magnetic beads. The swirling created by the addition of the Dynabeads magnetic beads in the lysis buffer will mix the components sufficiently. Vortexing or mixing further is not recommended as this will damage the DNA/Dynabeads complex.

What is the length of the DNA isolated by Dynabeads DNA Direct kits?

The isolated DNA is maintained at chromosome length during the lysis and washing steps. During these steps, it is important to take care not to break up the DNA/Dynabeads complex. The amount of shear force applied during resuspension determines the final average fragment length. Normally, the average fragment length exceeds 20 kb.

Can Dynabeads DNA Direct protocols be automated?

The properties of Dynabeads magnetic beads are excellent for automated liquid handling. Their protocols can be adapted to all automatic liquid handling instruments equipped with magnets.

How many isolations does the Dynabeads DNA Direct Universal kit support?

Dynabeads DNA Direct Universal kit (Cat. No. 63006) supports 300 isolations directly from crude material such as cultured cells, clinical specimens, bacteria, mouse tails, and other solid tissues from various species.

How does the Dynabeads DNA Direct Universal protocol work?

Dynabeads magnetic beads supplied in a lysis/binding buffer are added to sample, and DNA released from the lysed cells are adsorbed onto the surface of the Dynabeads magnetic beads during a brief incubation. This is followed by magnetic separation of the intact DNA/Dynabeads complex, removal of the supernatant, and subsequent washing to remove any residual contaminants and potential PCR inhibitors. Finally, the complex is resuspended for direct use in downstream PCR reactions. Pure DNA is extracted in only 10 min. Tedious centrifugation and precipitation steps are eliminated in this protocol.

What should I do if the A260/A280 ratio of my purified RNA is very low (e.g., <1.8)?

Check that you have not over-diluted the sample. That is, the A260 value is within the linear range of the spectrophotometer that you are using. Most spectrophotometers are only linear in the range 0.1 to 2.0 absorbance units.

If your sample has an A260 reading of less than 0.1 units, decrease the dilution of the sample, or read the undiluted sample and re-measure the A260/A280 ratio.

If the sample still has a low A260/A280 ratio, your sample may be contaminated with protein.

Be sure to do extra washes the next time you run that sample.

What is the detection limit when using Dynabeads magnetic beads for immunoprecipitation (IP)?

Answering this question is not straightforward. It will depend on the detection method. When using HRP (horseradish peroxidase)-based detection system or radioactivity in combination with a good antibody, very little target is required. More target is required when using an AP (alkaline phosphatase)-based detection system. When a sensitive detection system is used, detection will most likely be in the nanogram range. In some cases, pictograms of target can be detected.

Find additional tips, troubleshooting help, and resources within our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

What is the elution volume when using Dynabeads magnetic beads for immunoprecipitation (IP)?

Within practical limits, the elution volume can be scaled up or down to suit your experiment. However, volumes less than 10 µL become more difficult to work with. In addition, the amount of target is important. If you have a lot of beads with a lot of bound target in a small elution volume, your elution may not be very efficient. Typically, 15-100 µL of beads may be eluted in 30 µL. For efficient recovery of the antigen and/or binding partners, the elution volume should at minimum equal the volume of the beads.

Find additional tips, troubleshooting help, and resources within our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

How can I quantify the amount of antibody bound to Dynabeads magnetic beads?

There are several methods to quantify the amount of antibody bound to the beads. The crudest method is to measure the concentration of antibody in the coupling reaction before and after antibody attachment. Either fluorescence measurements or absorbance at 280 nm can be used. Alternatively, you could measure the amount of antibody bound to the beads by fluorescence, chemiluminescence, or radiolabeling detection methods.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

How long should I incubate my antibody with the lysates?

Incubation time will depend on the immunogenicity of the primary antibody and its binding affinity with the specific antigens. For a good primary antibody, 30-40 minutes incubation should work well. If you are working with a poor antibody or a very low-abundance protein, you could try to increase binding by incubating overnight. However, this also increases the chance of background protein binding.

Find additional tips, troubleshooting help, and resources within our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

When should I covalently bind the antibody to the Dynabeads surface?

If the target protein has the same molecular weight as the heavy or light chain antibody, we would recommend covalently binding the antibody to the bead surface. This can be done by either crosslinking the antibody to the Dynabeads Protein A or G magnetic beads, or secondary coated beads, or by using one of the surface-activated Dynabeads magnetic beads.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

What are the general advantages of using Dynabeads magnetic beads for protein isolation?

Using Dynabeads magnetic beads for protein isolation provides several advantages:

-Rapid binding kinetics: since the number of beads per volume for Dynabeads is approximately 1,000 times higher than for the same volume of a Sepharose slurry, the probability for Dynabeads magnetic beads to hit the target is far greater.

-Incubation time: due to the rapid binding kinetics, the protocol is usually very short.
-Low background: due to the rapid binding kinetics and the short incubation time, the background is also very low.
-Trapping of impurities: the beads offer no internal volume for binding or trapping of impurities.
-Low antibody consumption: this is because Dynabeads magnetic beads are nonporous, uniform superparamagnetic, monodispersed, highly crosslinked polystyrene microspheres consisting of an even dispersion of magnetic material throughout the bead. The beads are coated with a thin layer of a highly crosslinked polystyrene shell that encases the magnetic material and prevents any leakage from the beads or trapping of ligands in the bead interior. The outer layer also provides a defined surface area for the adsorption or coupling of various molecules such as antibodies. Uniformity of bead size and shape provide consistent physical and chemical properties. These uniform physical characteristics lead to high-quality, reproducible results.
-Reproducibility: due to easier practical handling, such as pipetting. No centrifugation steps or preclearing are required.

Find additional tips, troubleshooting help, and resources within ourProtein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

Are Dynabeads magnetic beads compatible with dithionite, DTT, and EDTA?

No. Not only is dithionite a reducing agent, but the strong affinity of the dithionite ion for bivalent and trivalent metal cations (M2+, M3+) allows it to enhance the solubility of iron, making it a chelating agent. As a result, the iron in the Dynabeads magnetic beads is reduced and pulled out when they are exposed to dithionite. The same is observed if Dynabeads magnetic beads are exposed to DTT and EDTA. With EDTA, we highly recommend checking the minimal amount of EDTA that your specific molecules would tolerate for binding to the Dynabeads, and if it will affect your specific application. For some applications, low concentrations of EDTA can be tolerated by Dynabeads. On the other hand, using 10 mM EDTA with heating affects the binding of biotin molecules to Dynabeads streptavidin.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

Are Dynabeads magnetic beads compatible with Urea?

Yes, they are compatible with 6-8 M Urea when used during post-coupling steps.

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.

Are Dynabeads magnetic beads compatible with centrifugation?

Dynabeads magnetic beads, being magnetic in nature are really not designed to be centrifuged. That being said, the beads themselves are compact, as the pores in the polymer matrix are filled with magnetic material and coated with a final outer polymer shell that will further add to the rigidity of the beads. Hence, pressure should theoretically not be a problem for the beads themselves, but the force exerted by the beads on surrounding cells in the pellet may be detrimental to the cells.

Find additional tips, troubleshooting help, and resources within our Dynabeads Nucleic Acid Purification Support Center as well as our Protein Immunoprecipitation (IP), Co-Immunoprecipitation (Co-IP), and Pulldown Support Center.

What are the benefits of using magnetic beads in immunoprecipitation (IP) experiments?

Magnetic beads, unlike agarose beads, are solid and spherical, and antibody binding is limited to the surface of each bead. While magnetic beads do not have the advantage of a porous center to increase the binding capacity, they are significantly smaller than agarose beads (1 to 4 µm), which collectively gives them adequate surface area-to-volume ratios for optimum antibody binding.

High-power magnets are used to localize magnetic beads to the side of the incubation tube and out of the way to enable cell lysate aspiration without the risk of also aspirating immune complexes bound to the beads. Magnetic separation avoids centrifugation, which can break weak antibody-antigen binding and cause loss of target protein.

However, an issue with the use of magnetic beads is that bead size variations may prevent all beads from localizing to the magnet. Additionally, while immunoprecipitation using agarose beads only requires standard laboratory equipment, the use of magnetic beads for immunoprecipitation applications requires high-power magnetic equipment that can be cost-prohibitive. Read more about our Magnetic Immunoprecipitation Products (https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-assays-analysis/immunoprecipitation.html#products).

Find additional tips, troubleshooting help, and resources within our Protein Assays and Analysis Support Center.