Zymo Research

<h2>What Are Cell-Free DNA Extraction Kits?</h2>
&nbsp;
A cell-free DNA (cfDNA) extraction kit purifies circulating cfDNA fragments from plasma, serum, or urine using silica spin-column or magnetic bead-based technologies. These kits are optimized to recover the short DNA fragments commonly found in liquid biopsy samples for downstream applications such as PCR, qPCR, next-generation sequencing (NGS), and methylation analysis. Choose a cfDNA-specific kit over a general genomic DNA kit whenever short circulating DNA fragments are the primary target.
&nbsp;
<h2>What you will find:</h2>
&nbsp;
<ul>
<li>MagBio cfKapture ccfDNA Extraction Kit: for cell-free DNA isolation using advanced magnetic bead-based technology.</li>
<li>MAGicBead&trade; cfDNA Isolation Kit: for automated, high-throughput liquid biopsy workflows using high-binding paramagnetic particles.</li>
<li>Quick-cfDNA&trade; Serum &amp; Plasma Kit: for streamlined manual benchtop purification using rapid spin-column technology.</li>
</ul>
&nbsp;
<h2>How to Choose a Cell-Free DNA Extraction Kit</h2>
&nbsp;
Input Volume Range
Choose a kit compatible with your typical plasma, serum, or urine input volume. Larger sample volumes generally increase total cfDNA recovery but may require additional reagents and longer processing times.
Column-Based vs. Magnetic Bead-Based Chemistry
Silica spin-column kits are widely used for manual purification workflows, while magnetic bead-based kits simplify automation and high-throughput processing on compatible liquid handling platforms.
Elution Volume for Downstream Assays
Select an elution volume that matches the input requirements of your downstream applications, such as PCR, qPCR, or NGS library preparation, to minimize additional concentration or dilution steps.
Combined DNA/RNA Recovery
If your workflow requires analysis of both circulating DNA and RNA from the same specimen, consider kits designed to recover multiple nucleic acid types from a single sample.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
Key considerations when selecting a cell-free DNA extraction kit include sample input volume, purification chemistry, compatibility with manual or automated workflows, and elution volume for downstream molecular assays. Magnetic bead-based systems are commonly selected for scalable, automated liquid biopsy workflows, while spin-column kits provide reliable manual purification for routine laboratory use. The optimal kit depends on your sample type, throughput requirements, and downstream analytical methods.
<section class="mbp-contact-cta">
&nbsp;
MBP's specialist team can help match kit chemistry, format, and throughput to your sample type and downstream application.&nbsp;<a href="https://mbpinc.net/contact-us">Contact the MBP team</a> for personalized guidance.
</section>

Cell-Free DNA

Brochure

D4086-MSDS

D4086-4-MSDS

D4086-5-MSDS

D4086-Quick Protocol

D4086-Protocol

D4086-Automation Notes

MAGicBead™ cfDNA Isolation Kit

The MAGicBead™ cfDNA Isolation Kit by Zymo Research isolates NGS-ready cell-free DNA from up to 10 mL of plasma, saliva, urine, or other biofluids using magnetic bead technology, eluting in ≥15 µl with a 140–170 bp mono-nucleosomal peak. Compatible with KingFisher, Hamilton STAR, Tecan Fluent, and Opentrons OT-2. Available as D4086 (50 Preps. kit), D4086-4-70 (cfDNA Wash Buffer 70 mL), and D4086-5-2 (cfDNA Elution Buffer 2 mL).

Elution Volume

Fragment Sizes

Processing Time

Purity

Required Equipment

Sample Compatibility

Yield

Manufacturer

Shipping Condition

Storage Condition

MAGicBead™ cfDNA Isolation Kit (50 Preps.)

MAGicBead™ cfDNA Wash Buffer (70 ml)

MAGicBead™ cfDNA Elution Buffer (2 ml)

<h2>What are bisulfite conversion reagents and buffers?</h2>
&nbsp;
Bisulfite conversion reagents include sodium bisulfite solution, denaturation and conversion buffers, and complete kits that bundle all components needed for the three-step chemical reaction: sulfonation of cytosine to a cytosine-bisulfite derivative, hydrolytic deamination to a uracil-bisulfite derivative, and alkali desulfonation to yield uracil. This process converts unmethylated cytosines to uracil while leaving 5-methylcytosine intact and unconverted, because 5-methylcytosine resists bisulfite-mediated deamination under standard conditions.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">RNA and DNA conversion reagents for enhanced modification of cytosine in methylation workflows</li>
<li dir="ltr" role="presentation">Desulphonation buffers for stabilization of nucleic acids and post-conversion cleanup&nbsp;</li>
<li dir="ltr" role="presentation">Binding buffers used during purification for efficient capture of converted RNA and DNA</li>
<li dir="ltr" role="presentation">Wash buffers for the removal of inhibitors and improved purity of samples</li>
<li dir="ltr" role="presentation">Elution buffers for high-quality recovery of converted nucleic acids</li>
<li dir="ltr" role="presentation">DNA denaturing and digestion buffers for controlled workflow and optimized conversion efficiency</li>
<li dir="ltr" role="presentation">Dilution and reaction buffers for maintaining stable assay conditions</li>
<li dir="ltr" role="presentation">Solubilization and dissolution buffers for sample processing and preparation&nbsp;</li>
<li dir="ltr" role="presentation">Lightning conversion reagents for efficient and rapid methylation analysis workflows</li>
</ul>
&nbsp;
<h2>How to use bisulfite conversion reagents</h2>
&nbsp;
Ensure complete DNA denaturation before conversion to avoid incomplete conversion
Bisulfite only acts on cytosines in single-stranded DNA, so complete denaturation of the input DNA is the most critical first step, since failure to fully denature can leave double-stranded regions in which cytosines are shielded from the bisulfite reagent and remain unconverted.
Understand that incomplete conversion produces false-positive methylation results
If the conversion is incomplete, unconverted unmethylated cytosines will read as cytosine after sequencing, which will be incorrectly interpreted as methylated cytosine, artificially inflating the apparent methylation level of the sample in a false-positive direction.
Optimize conversion conditions to balance completeness against DNA degradation
The harsh conditions needed for complete bisulfite conversion, including high bisulfite concentration, elevated temperature, and long incubation, also fragment and degrade DNA, and optimizing conditions that achieve high conversion while minimizing degradation is a key technical challenge in bisulfite workflows.
Include an unmethylated conversion control to estimate residual incomplete conversion
Including an unmethylated control DNA, such as lambda phage DNA, in the same conversion reaction provides a readout of how completely unmethylated cytosines were converted, helping quantify residual incomplete conversion rates and account for them in downstream analysis.
Be aware of specific challenges for FFPE and degraded DNA samples
Formalin-fixed, paraffin-embedded tissue DNA is already fragmented before bisulfite treatment, and the additional fragmentation during conversion can result in poor library yields; specific modified protocols and carrier reagents can help reduce further degradation during the conversion step.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
Bisulfite sequencing is widely regarded as the gold standard for DNA methylation analysis due to its high resolution and accuracy at single-base level, but it also introduces specific DNA quality challenges for downstream library preparation and sequencing, particularly for samples already of poor quality like FFPE tissue. As of 2026, enzymatic conversion is increasingly recommended as the preferred alternative to bisulfite conversion specifically because it achieves comparable discrimination between methylated and unmethylated cytosines while minimizing the DNA damage and library complexity loss that harsh bisulfite chemistry introduces.
This category sits within DNA/RNA Methylation under Epigenetics, and for a synthetic, fully methylated positive control to run through the conversion workflow, see dNTPs (Deoxynucleotide Triphosphates). See the full reagents catalog and use Quick Order for recurring orders.
<a href="https://mbpinc.net/contact-us">Contact the expert team</a> at MBP and request a quote today to get high-quality bisulfite conversion reagents for your lab.

Bisulfite Conversion Reagents & Buffers

D5001-3-MSDS

M-Binding Buffer

M-Binding Buffer is available in the following variants: D5001-3, D5002-3, D5040-3, D5049-3.The D5001-3 by Zymo Research is M-Binding Buffer (20 ml), the Zymo-Spin column binding reagent for purification of bisulfite-converted DNA in EZ DNA Methylation, EZ DNA Methylation-Gold, EZ DNA Methylation-Direct, and EZ DNA Methylation-Lightning kits. Sold as a standalone replacement buffer for labs running high-volume bisulfite conversion workflows. Made in the USA.

M-Binding Buffer (20 ml)

M-Binding Buffer (80 ml)

M-Binding Buffer (250 ml)

M-Binding Buffer (100 ml)

D5005-3-MSDS

M-Binding Buffer-Gold

Zymo Research M-Binding Buffer-Gold for bisulfite-converted DNA column binding in EZ DNA Methylation-Gold Kit (D5005/D5006). Two volumes: D5005-3 (30 mL) and D5006-3 (125 mL).

M-Binding Buffer-Gold (30 ml)

M-Binding Buffer-Gold (125 ml)

M-Desulphonation Buffer

Zymo Research M-Desulphonation Buffer: in-column desulphonation of bisulfite-converted DNA for EZ DNA Methylation Kit, Methylation-Gold Kit, and Methylation-Direct Kit. Three volumes: D5001-5 (10 mL), D5002-5 (40 mL), D5040-5 (80 mL).

M-Desulphonation Buffer (10 ml)

M-Desulphonation Buffer (40 ml)

M-Desulphonation Buffer (80 ml)

MSDS

M-Digestion Buffer

D5020-9 by Zymo Research — M-Digestion Buffer (2X); 4 mL; proteinase K digestion buffer for EZ DNA Methylation-Direct workflows; 50 pg–2 µg DNA input; compatible with blood, tissue, FFPE, LCM; 50°C 20 min (standard) or 4 hr (FFPE).

M-Digestion Buffer (2X) (4 ml)

M-Digestion Buffer (2X) (15 ml)

D5001-2-MSDS

M-Dilution Buffer

Zymo Research M-Dilution Buffer for EZ DNA Methylation Kit: DNA denaturation (5 µl/sample) and CT Conversion Reagent preparation (210 µl/tube). Two volumes: D5001-2 (1.3 mL) and D5002-2 (5.2 mL).

M-Dilution Buffer (1.3 ml)

M-Dilution Buffer (5.2 ml)

D5005-2-MSDS

M-Dilution Buffer-Gold

Zymo Research M-Dilution Buffer-Gold: CT Conversion Reagent rehydration buffer for EZ DNA Methylation-Gold Kit (D5005/D5006) only. Two volumes: D5005-2 (1.5 mL) and D5006-2 (7 mL).

M-Dilution Buffer-Gold (1.5 ml)

M-Dilution Buffer-Gold (7 ml)

D5005-6-MSDS

M-Dissolving Buffer

Zymo Research M-Dissolving Buffer for reconstituting the CT Conversion Reagent in the EZ DNA Methylation-Gold Kit (D5005/D5006). Two volumes: D5005-6 (500 µl) and D5006-6 (1.2 mL).

M-Dissolving Buffer (500 µl)

M-Dissolving Buffer (1.2 ml)

D5001-6 - MSDS

M-Elution Buffer

The M-Elution Buffer by Zymo Research is the dedicated elution buffer for bisulfite-converted DNA from EZ DNA Methylation spin columns, compatible with EZ DNA Methylation, EZ DNA Methylation-Gold, EZ DNA Methylation-Direct, and EZ DNA Methylation-Lightning kits. Available as D5001-6 (1 ml), D5002-6 (4 ml), D5007-6 (8 ml), and D5041-6 (40 ml).

M-Elution Buffer (1.0 ml)

M-Elution Buffer (4 ml)

M-Elution Buffer (8 ml)

M-Elution Buffer (40 ml)

M-Elution Buffer (50 ml)

D5049-6 by Zymo Research is M-Elution Buffer (50 mL) for eluting bisulfite-converted DNA from Zymo-Spin columns in EZ DNA Methylation, EZ DNA Methylation-Gold, EZ DNA Methylation-Direct, and EZ DNA Methylation-Lightning Kit workflows — 10 µL per column elution. Eluate is ready for immediate use or storage at ≤–20°C.

<h2>What are methylation standards?</h2>
&nbsp;
Methylation standards are defined reference DNA materials with a known and confirmed methylation status, ranging from a fully methylated DNA (where every cytosine at CpG or other sites carries a methyl group) to a fully unmethylated DNA (where no cytosines are methylated) and intermediate or mixed standards containing a defined ratio of the two. The most widely used unmethylated control in bisulfite sequencing is lambda phage DNA, which is naturally unmethylated and can be spiked into a conversion reaction to estimate conversion efficiency.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">Methylated and non-methylated DNA control sets for comparative epigenetic analysis and assay validation</li>
<li dir="ltr" role="presentation">Universal methylated DNA standards for methylation assessment workflows</li>
<li dir="ltr" role="presentation">Genomic DNA reference materials: for microbial and human methylation studies</li>
<li dir="ltr" role="presentation">Matched DNA sets: used in experimental models for controlled comparison of methylation status&nbsp;</li>
<li dir="ltr" role="presentation">Bisulfite-converted DNA standards: for downstream sequencing-based methylation and PCR analysis</li>
<li dir="ltr" role="presentation">Methylation spike-in controls: for sequencing normalization and high-throughput workflows</li>
<li dir="ltr" role="presentation">Mouse and human DNA methylation reference sets: for specific species epigenetic studies</li>
<li dir="ltr" role="presentation">Methylated DNA IP control kits for methylation assays involving immunoprecipitation</li>
</ul>
&nbsp;
<h2>How to use methylation standards</h2>
&nbsp;
Spike an unmethylated control into every bisulfite or enzymatic conversion reaction
Running an unmethylated DNA like lambda phage DNA alongside your samples in the same conversion reaction estimates the conversion efficiency of that specific run, since every remaining cytosine signal after conversion should be treated as a false positive, and this rate can be quantified and accounted for in downstream analysis.
Run a fully methylated positive control to confirm methylated cytosines are preserved
A fully methylated standard, such as DNA synthesized with 5-methyl-dCTP or commercially prepared methylated genomic DNA, confirms your conversion workflow correctly preserves methylated cytosines intact rather than inadvertently converting them, which would produce false-negative methylation calls.
Use a mixed or intermediate standard to calibrate quantitative methylation assays
A standard containing a defined ratio of methylated to unmethylated DNA, or a set of standards spanning a range of methylation percentages, provides a calibration curve for quantitative methylation assays like 5-methylcytosine ELISA, validating that the assay reports the expected methylation level across its full dynamic range.
Confirm standard stability before long-term storage or lot-to-lot use
Methylation control DNA has documented stability windows, and confirming that your standard's methylation status is stable under storage conditions, and consistent across lots, is necessary for reliable longitudinal monitoring of conversion efficiency.
Use standards to monitor workflow consistency over time
Running a conversion control in every batch allows longitudinal tracking of conversion efficiency across instrument runs, reagent lots, and protocol variations, helping catch workflow drift before it affects real sample results.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
Lambda phage DNA is the most commonly used unmethylated bisulfite conversion control because it is naturally unmethylated, commercially available, and well characterized, and it can be aligned to the known lambda phage reference genome after sequencing to calculate residual unconverted cytosine rates, providing a direct, interpretable measure of conversion efficiency. As of 2026, fully methylated and fully unmethylated standard sets are also used alongside enzymatic methyl-seq conversions to confirm that EM-seq's enzymatic mechanism correctly protects methylated cytosines and converts unmethylated ones, independent of the conversion chemistry used.
This category sits within DNA/RNA Methylation, alongside Bisulfite Conversion Kits, Non-Bisulfite Kits &amp; Reagents, and ELISA Kits &amp; Reagents. See the full reagents catalog and use Quick Order for recurring orders.
<a href="https://mbpinc.net/contact-us">Contact the expert team of Molecular Biology Products Inc. (MBP)</a> to get high-quality methylation standards for your lab today.

Methylation Standards

Protocol

Methylated & Non-methylated pUC19 DNA Set

D5017 by Zymo Research provides paired methylated and non-methylated pUC19 plasmid DNAs (1 ng/µl each, linearized by ScaI) plus pUC19MN primers for monitoring bisulfite conversion efficiency and calibrating DNA methylation quantitation assays. The methylated variant is fully CpG-methylated via CpG Methylase; the non-methylated variant is propagated in a Dam⁻/Dcm⁻ strain, ensuring no residual Dam or Dcm methylation. Suitable for WGBS spike-in, targeted bisulfite sequencing QC, and methylation standard curve construction.

Additional Info

Concentration

Storage

Methylated-DNA IP Kit (10 Rxns.)

The D5101 by Zymo Research is a 10-reaction Methylated-DNA IP Kit for immunoprecipitation of 5mC-containing DNA from 50–500 ng fragmented genomic input, achieving &gt;100-fold methylated DNA enrichment using Anti-5-Methylcytosine Monoclonal Antibody Clone 7D21. The full workflow completes in approximately 4 hours and eluted DNA is compatible with MeDIP-seq, bisulfite sequencing, PCR, and microarray analysis.