Kits, Reagents, and Protocols

Use the MagMAX FFPE DNA/RNA Ultra Kit for fast, reliable nucleic acid isolation from FFPE samples. You can even extract DNA and RNA sequentially from the same sample in a single workflow, drawing richer data from your precious samples. For example, you can investigate important biomarkers, such as hotspot mutations, CNVs, gene fusions, and indels.

The kit has been validated for multiple research sample types, including solid tumor biopsies, core needle biopsies, and fine-needle aspirates. It is also compatible with CitriSolv™ clearing agent, a deparaffinization alternative to xylene that is less toxic and can be used without a chemical fume hood.

To speed up the deparaffinization process, pair the FFPE DNA/RNA Ultra Kit with the Applied Biosystems™ AutoLys™ system. Comprised of pretreated tubes and a rack system to help reduce pipetting steps, AutoLys tubes and accessories eliminate the need for hazardous chemicals and helps minimizes loss of tissue sample.

Liquid biopsies most often utilize cell-free DNA (cfDNA) that is derived from both normal and cancerous cells. The tumor-only supply of DNA in the bloodstream is more commonly referred to as circulating tumor DNA (ctDNA), which is loaded with information about a tumor that would otherwise be difficult to access. In these kits, magnetic beads and optimized chemistry combine for efficient nucleic acid isolation that specifically recovers the fragmented cfDNA while leaving the larger DNA molecules behind. This aspect of enrichment for the cfDNA portion of the total nucleic acid ensures that the shorter, ctDNA is concentrated and ready for downstream analysis using qPCR, digital PCR (dPCR), or next-generation sequencing (NGS).

While the importance of cfDNA is becoming established, it may not tell the whole story. cfRNA sequences serve as critical biomarkers in the form of microRNAs and gene fusions. The inclusion of cfRNA with cfDNA in the Total Nucleic Acid Kit provides an opportunity for researchers to expand their studies and advance human health.

Use the MagMAX Cell-Free DNA Isolation Kit with KingFisher instruments, Oncomine assays, and other downstream applications to optimize the liquid biopsy workflow from extraction and purification to analysis.

Use the MagMAX Cell-Free Total Nucleic Acid Isolation Kit to extend your liquid biopsy workflow to include both cell-free DNA and RNA (cfRNA) from the same sample.

Use the MagMAX DNA Multi-Sample Ultra 2.0 Kit to recover high-purity gDNA from both small- and large-volume inputs. The kit produces maximum yield by treating samples with proteinase K (PK) and P-enhancer, followed by an innovative lysis/binding solution to simultaneously lyse cells, denature proteins, and capture gDNA on the high-binding magnetic beads. Designed for flexibility, the kit allows you to skip sample and buffer volume normalization steps for trouble-free processing. For example, you can run 50–µL and 400–µL samples at the same time on the same plate.

Reagents for the MagMAX DNA Multi-Sample Ultra 2.0 Kit are also available in bulk, allowing you to process 2,000 50–200 µL samples or 1,000 200–400 µL samples.

KingFisher Ready DNA Ultra 2.0 Prefilled Plates contain the same reagents and produce the same high-quality results as the MagMAX DNA Multi-Sample Ultra 2.0 Kit, but the plates are already conveniently filled with reagents. This eliminates the need to dispense lysis, wash solutions, and magnetic beads. The protocol is simple: just peel off the foil, add sample and enhancer/Proteinase K solutions, and insert into the instrument.

Use the MagMAX gDNA Saliva Kit with KingFisher instruments to recover high-purity gDNA from saliva samples. The kit treats samples with an innovative lysis/binding solution to simultaneously lyse cells, denature proteins, and capture gDNA on the high-binding magnetic beads. Designed for flexibility, the kit allows you to skip sample and buffer volume normalization steps for trouble-free processing. For example, you can run 50-µL and 400-µL samples at the same time on the same plate. The workflow is compatible with saliva collection devices like the Oragene® from Genotek, the GeneFiX™ from IsoHelix, and the SalivaGard® from Biomatrica.

Use the MagMAX mirVana Total RNA Isolation Kit for low- or high-throughput isolation of true total RNA that covers the full range of RNA types present in cells, from small RNAs such as microRNAs (miRNAs) to non-coding RNA, messenger RNA, and ribosomal RNA. The kit elutes highly concentrated RNA in as little as 20 µL of nuclease-free water and its chemistry stabilizes and preserves RNA over time.

The extracted RNA is suitable for a range of downstream gene expression applications such as miRNA-Seq and qRT-PCR. Workflows have been validated for the TaqMan™ Advanced miRNA cDNA Synthesis Kit and other TaqMan Advanced miRNA Assays.

The human microbiome is complex and multifaceted, and each body habitat harbors different dominant signature taxa. The gut contains the bulk of microbiota associated with the human body and has been one of its most thoroughly examined ecosystems. Fecal samples are commonly used for these analyses because they are easy to obtain and contain a large amount of biomass. Body fluids like saliva and urine are less studied, but each contains unique bacterial communities.

Use the MagMAX Microbiome Ultra Nucleic Acid Isolation Kit to isolate the total nucleic acid from feces, urine, saliva, and other samples. It can extract high-yield, high-purity, high-quality, inhibitor-free DNA and RNA that is excellent for metagenomics research and other downstream applications. Enzyme-based digestion allows recovery of nucleic acids from a wide range of microorganisms without additional processing steps.

The kit can isolate both viral and bacterial nucleic acids, and has been tested with mammalian, reptilian, fish, and bird fecal samples; VTM, skin, and milk samples; and yeast and bacterial cultures. It is recommended for research labs that are developing their own microbiome tests, conducting microbiome research using soil, stool, swabs and environmental sample types and need low- and/or high-throughput solutions for isolating total nucleic acid.

The MagMAX Prime Viral/Pathogen NA Isolation Kit is an exceptional kit when testing for human microbiome applications. It utilizes our most advanced formulation to isolate high quality of nucleic acid from sample types such as stool.

The MagMAX Wastewater Ultra Nucleic Acid Isolation Kit is an automation-compatible extraction kit optimized to extract viral nucleic acids from wastewater, sewage, and sludge. Versions of the kit are available with and without Applied Biosystems Dynabeads Wastewater Virus Enrichment beads to concentrate your wastewater sample.

The MagMAX Wastewater Ultra Nucleic Acid Isolation Kit (Cat. No. A52606) enables efficient, high-throughput nucleic acid extraction from 200 µL to 500 mL of wastewater samples. The kit is also compatible with samples that have been concentrated by ultracentrifugation or precipitation or with non-concentrated samples, designed to help ensure reproducible recovery of high-quality nucleic acids compatible with a broad range of applications such as real-time PCR and next-generation sequencing.

The MagMAX Wastewater Ultra Nucleic Acid Isolation Kit with Virus Enrichment (Cat. No. A52610) utilizes Dynabeads and MagMAX magnetic-bead technology to allow for automated virus enrichment. Up to 10 mL of wastewater can be processed, with virus concentration followed by extraction.

MagMAX Prime Viral/Pathogen NA Isolation Kit utilizes our most advanced formulation to isolate nucleic acids from a diverse range of biological specimens. It enables a streamlined workflow with easy-to-follow protocols using a single user guide while also allowing users to run various sample types on a single plate via the same KingFisher script. This kit is available in user-filled, prefilled, accessories and bulk format.

MagMAX viral/pathogen kits are designed for high nucleic acid recovery and are compatible with low-titer samples. There are only two protocols for low- to high-volume input range. No carrier is required, which means less interference with downstream applications and fewer required steps.

MagMAX Viral/Pathogen Nucleic Acid Isolation Kits I and II (MVP I and II) are recommended for use by research labs. Both kits have been validated with newly developed, streamlined protocols allowing a sample input volume of 200 µL (vs standard 400 µL) with half the amount of extraction reagents.

The two MagMAX kits are functionally identical, as are the chemistry driving the RNA to the beads and the overall workflow. The two differences are: (a) A raw material change in the bead component due to unprecedented SARS-CoV-2 demand, and (b) The MVP II kit is available only in bulk prep format.

Plant cell walls can be very difficult to disrupt and lysates often contain significant amounts of compounds such as tannins, phenolics, and complex polysaccharides that can affect nucleic acid quality and inhibit downstream reactions. Despite these challenges, these MagMAX kits can effectively isolate DNA or RNA from diverse plant samples such as Arabidopsis thaliana, bell pepper leaves, canola/rapeseed leaves, corn leaves, green onion, lemon leaves, oat leaves, orange, pine needles, spinach leaves, tomato leaves, and wheatgrass leaves.

Use the MagMAX Plant DNA and RNA Kits with KingFisher instruments for automated purification of DNA and RNA from a wide variety of plant species and tissue types, including plant fungus. Purified DNA or RNA is free of proteins, nucleases, and other contaminants, inhibitors, and nucleic acids, and can be used in a wide range of downstream applications such as PCR, qPCR, and NGS. The kits are optimized for isolation of DNA and RNA from 10–100 mg of plant samples.

There are two variations on the IP process. If your target protein is abundant, you can use the direct method, in which the primary antibody (Ab) is first incubated with the Dynabeads magnetic beads, followed by a wash to remove unbound antibodies. The Ab-bound beads are then incubated with with the sample for capture, followed by washing and elution.

If the target protein is not abundant, you can use the indirect method, in which the primary Ab is first incubated with the cell lysate to form an Ab-antigen complex. The complex is then captured by adding Dynabeads beads to the sample, followed by washing and elution.

Although IP can be performed manually, the number of washing steps and the hands-on time increase proportionally with the number of samples. Automating the process with KingFisher instruments can eliminate inconsistencies introduced by pipetting and other manual handling. The automated protocols replicate the manual protocols, obtaining equally high target protein yield and the same low non-specific binding and high reproducibility. Whether you are working with 10 or 96 samples, the IP protocol takes less than 40 minutes. Just load the reagents on the plates, push the Start button, and by the time you have prepared for downstream analysis, the IP is done. Some optimization, such as incubation time, might be necessary depending on your Ab and the abundance and/or specificity of your target protein.

Deciding among the kits depends on the target protein you need to isolate. If you have a primary antibody to the protein, we recommend using Dynabeads Protein A or G or their associated kits. If you have a secondary antibody, use one of the Dynabeads M-280 IgG products. Finally, if you have a biotinylated antibody or ligand, use Dynabeads M-280 Streptavidin. 

Thermo Scientific SMART Digest Kits paired with KingFisher instruments represent the latest advance in automated protein digestion for peptide mapping and quantitation applications. The kits help make protein digestion fast, simple, reproducible, and easy to automate.

The protein digestion kits use optimized heat-stable enzymes on magnetic beads, helping minimize the possibility of post-translational modifications. Automating the process minimizes manual handling, helps ensure the optimal timing of reactions, and reduces high-temperature exposure, increasing reproducibility of results.^[1]

Immunoaffinity (IA) kits couple enzymatic digestion with IA capture on a single bead for high sensitivity. This innovation helps generate confidence in your high-performance liquid chromatography (HPLC) and liquid chromatography/mass spectrometry (LC/MS) results. SMART Digest Kits especially benefit biomarker and biopharmaceutical characterization and quantitation applications.

For peptide mapping applications, choose among optimized heat-stable trypsin, chymotrypsin, or proteinase K enzymatic digestion for sequence-specific cleavage of your protein. The enzyme, on magnetic beads, is activated at elevated temperatures for accelerated digestion under protein denaturing conditions.

• Trypsin cleaves the C-terminal side of lysine and arginine amino acid residues
• Chymotrypsin cleaves the peptide bonds formed by aromatic residues such as tyrosine, phenylalanine, and tryptophan
• Proteinase K cleaves the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids with blocked alpha amino groups

For peptide quantitation applications, SMART Digest IA Kits perform trypsin digestion with immunoaffinity capture in a single well. The immunoaffinity moiety (streptavidin, protein A, or protein G) is typically employed to increase sensitivity by purifying your low-level proteins from complex biological matrices.