Zymo Reagents

<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.
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<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

M-Desulphonation Buffer

D5001-5 by Zymo Research is M-Desulphonation Buffer (10 ml), the in-column desulphonation reagent for the EZ DNA Methylation Kit, EZ DNA Methylation-Gold Kit, and EZ DNA Methylation-Direct Kit. It is ordered as a standalone replacement when this component is depleted before other kit contents. Also available in 40 ml (D5002-5) and 80 ml (D5040-5) formats.

Manufacturer

Shipping Condition

Storage Condition

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

D5001-2 by Zymo Research is M-Dilution Buffer (1.3 mL) — a required component of the EZ DNA Methylation Kit used to prepare DNA samples for bisulfite conversion (5 µL per reaction) and to dissolve CT Conversion Reagent (210 µL per tube). Sold separately for component replenishment.

M-Dilution Buffer (1.3 ml)

M-Dilution Buffer (5.2 ml)

D5005-2-MSDS

M-Dilution Buffer-Gold

The D5005-2 by Zymo Research is M-Dilution Buffer-Gold (1.5 ml), used exclusively to prepare the CT Conversion Reagent in the EZ DNA Methylation-Gold Kit for bisulfite conversion of genomic DNA. Sold as a standalone replacement when this component is depleted before other kit reagents. Made in the USA; not interchangeable with M-Dilution Buffer from the standard EZ DNA Methylation kit.

M-Dilution Buffer-Gold (1.5 ml)

M-Dilution Buffer-Gold (7 ml)

D5005-6-MSDS

M-Dissolving Buffer

D5005-6 by Zymo Research is a 500 µl standalone M-Dissolving Buffer for preparing the CT Conversion Reagent in the EZ DNA Methylation-Gold Kit (D5005/D5006). It dissolves the lyophilized reagent into a homogeneous working solution and is available separately for component replenishment. Stored at room temperature. Incompatible with EZ DNA Methylation Kit (D5001), which uses a different buffer formulation.

M-Dissolving Buffer (500 µl)

M-Dissolving Buffer (1.2 ml)

D5001-6 - MSDS

M-Elution Buffer

D5001-6 M-Elution Buffer by Zymo Research — 1 ml; dedicated elution buffer for bisulfite-converted DNA; compatible with EZ DNA Methylation, EZ DNA Methylation-Gold, EZ DNA Methylation-Direct, and EZ DNA Methylation-Lightning kits.

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.

M-Reaction Buffer

D5020-8 M-Reaction Buffer by Zymo Research is a 1 ml replacement component for the EZ DNA Methylation-Direct Kit, stored at room temperature. Used at 160 µl per CT Conversion Reagent preparation in bisulfite conversion workflows.

M-Reaction Buffer (1 ml)

M-Reaction Buffer (4 ml)

M-Solubilization Buffer

M-Solubilization Buffer (D5020-7) by Zymo Research — 4.5 ml reagent for dissolving the CT Conversion Reagent in the EZ DNA Methylation-Direct Kit. Stored at room temperature; sold separately or as a kit component. Made in the USA.

M-Solubilization Buffer (4.5 ml)

M-Solubilization Buffer (18 ml)

D5001-4 - MSDS

M-Wash Buffer

D5001-4 by Zymo Research is a 6 mL M-Wash Buffer used in the wash step of bisulfite-converted DNA purification across the EZ DNA Methylation, EZ DNA Methylation-Gold, EZ DNA Methylation-Direct, and EZ DNA Methylation-Lightning kit series.

M-Wash Buffer (6 ml)

M-Wash Buffer (24 ml)

M-Wash Buffer (72 ml)

M-Wash Buffer (36 ml)

<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

MAGicBead™ cfDNA Isolation Kit D4086 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.

Elution Volume

Fragment Sizes

Processing Time

Purity

Required Equipment

Sample Compatibility

Yield

MAGicBead™ cfDNA Isolation Kit (50 Preps.)

MAGicBead™ cfDNA Wash Buffer (70 ml)

MAGicBead™ cfDNA Elution Buffer (2 ml)

MIP Buffer (20 ml)

D5101-3-20 by Zymo Research is the MIP Buffer (20 mL), the immunoprecipitation reaction buffer for the Methylated-DNA IP Kit (D5101). Formulated for antibody-mediated enrichment of 5-methylcytosine-containing DNA in MeDIP, MeDIP-Seq, and MeDIP-qPCR workflows. Store at 0°C to room temperature; do not freeze.

United States

Texas

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