Zymo Research

<h2>What are bisulfite conversion kits?</h2>
&nbsp;
Bisulfite conversion kits are all-in-one systems that bundle every reagent and column needed for the sodium bisulfite conversion workflow into a single, pre-optimized format, covering the denaturation and sulfonation steps, desulfonation with an alkali reagent, and a post-conversion cleanup step that removes the bisulfite and other reaction byproducts before the converted DNA is used in downstream analysis. This contrasts with standalone Bisulfite Conversion Reagents &amp; Buffers, which lets labs assemble their own optimized protocol from individual components.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Standard bisulfite conversion kits for routine DNA methylation analysis&nbsp;</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Combined transcriptomic and epigenetic studies with RNA and DNA methylation conversion kits</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">High-throughput 96-well bisulfite conversion kits for wider-scale screening applications</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Automation-compatible bisulfite kits for simplified workflow integration</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Magnetic bead-based bisulfite conversion kits for enhanced purification and recovery efficiency</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Direct bisulfite conversion kits for streamlined sample processing&nbsp;</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Rapid conversion kits for methylation analysis workflows that are time-sensitive&nbsp;</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Starter kits for validation and optimized setup of bisulfite conversion protocols</li>
</ul>
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<h2>How to choose a bisulfite conversion kit</h2>
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Match kit format to your downstream sequencing or PCR application
Kit versions optimized for WGBS work at larger input scales with library prep in mind, while RRBS-compatible kits often include restriction enzyme digestion components to enrich CpG-dense regions before conversion, and MSP-focused kits may include primers or protocol guidance for post-conversion methylation-specific PCR.
Check the kit's validated input DNA range against your sample type
Different bisulfite conversion kits are validated for different input DNA ranges, and kits validated for low-input or cell-free DNA samples specifically address the additional fragmentation and yield challenges that these sample types face during the harsh chemical conversion step.
Confirm the kit includes an unmethylated conversion control or specify one separately
A quality bisulfite conversion kit should provide, or clearly specify, an unmethylated control to run alongside samples, since tracking conversion efficiency across the kit's components helps catch kit-specific variability in conversion completeness between different lots or runs.
Consider kits with optimized FFPE protocols when working with formalin-fixed tissue
Formalin-fixed, paraffin-embedded tissue DNA is already fragmented before conversion; kits with FFPE-specific protocol variants include modifications like shortened incubation times and carrier reagents to minimize the further fragmentation this already-compromised input type would suffer under standard conversion conditions.
Evaluate throughput format options to match your sample volume
Some bisulfite conversion kits are available in spin column formats suited to individual sample processing, while plate-based or automation-compatible formats support higher-throughput sample sets, making format an important practical consideration beyond kit chemistry alone.
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<h2>Specifications context</h2>
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Bisulfite sequencing is widely regarded as the gold standard for DNA methylation analysis at single-base resolution, and a key advantage of using a complete kit over standalone reagents is that the included cleanup step reliably removes residual bisulfite and salt from the converted DNA, which would otherwise inhibit downstream PCR amplification and library preparation. As of 2026, enzymatic conversion kits (covered in Non-Bisulfite Kits &amp; Reagents) are increasingly positioned as an alternative that avoids the DNA damage introduced by chemical bisulfite treatment, though bisulfite conversion kits remain broadly used and well-validated across the largest range of downstream applications.
<a href="https://mbpinc.net/contact-us">Contact the expert team</a> at MBP and get high-quality bisulfite conversion kits for your lab.

Bisulfite Conversion Kits

D5032-Data Sheet

D5032-MSDS

D5032-Protocol

D5033-Protocol

D5032-App Note (Hamilton)

EZ-96 DNA Methylation-Lightning™ Kit

The EZ-96 DNA Methylation-Lightning™ Kit is available in the following variants: D5032, D5033.EZ-96 DNA Methylation-Lightning™ Kit (D5032) by Zymo Research converts 100 pg–2 µg DNA with &gt;99.5% bisulfite conversion efficiency in 1.5 hours across a 96-well plate format (2×96 rxns/kit). &gt;80% recovery, &gt;50 bp fragments, Hamilton-automation compatible. Available from MBP Inc.

Applications

Conversion

Elution Volume

Equipment

Input

Processing Time

Recovery

Sample Source

Manufacturer

Shipping Condition

Storage Condition

EZ-96 DNA Methylation-Lightning™ Kit (Shallow-Well) (2 x 96 Rxns.)

EZ-96 DNA Methylation-Lightning™ Kit (Deep-Well) (2 x 96 Rxns.)

D5004-Protocol

MSDS

D5003-Protocol

D5003-App Note

EZ-96 DNA Methylation™ Kit

The EZ-96 DNA Methylation™ Kit is available in the following variants: D5003, D5004.D5003 by Zymo Research is a 2 × 96 reaction bisulfite conversion kit in shallow-well format for high-throughput DNA methylation analysis. Converts &gt;99% of unmethylated cytosines to uracil; protects &gt;99% of methylated cytosines; &gt;80% DNA recovery in ≥30 µl. Accepts 500 pg–2 µg input DNA per well. Compatible with MSP, WGBS, RRBS, pyrosequencing, and Illumina methylation arrays.

EZ-96 DNA Methylation™ Kit (Shallow-Well) (2 x 96 Rxns.)

EZ-96 DNA Methylation™ Kit (deep-well) (2 x 96 Rxns.)

DataSheet

Protocol

App Note

EZ-96 DNA Methylation™ MagPrep

Zymo Research EZ-96 DNA Methylation™ MagPrep: 96-well magnetic bead bisulfite conversion, 500 pg–2 µg input, &gt;99% efficiency, &gt;70% recovery, 12–16 hr. D5040 (4×96 = 384 rxns) and D5041 (8×96 = 768 rxns).

EZ-96 DNA Methylation™ MagPrep (4 x 96 Rxns.)

EZ-96 DNA Methylation™ MagPrep (8 x 96 Rxns.)

Devices & Instruments

EZ-Vac Vacuum Manifold

EZ-Vac Vacuum Manifold (S7000) by Zymo Research — processes 1–20 Zymo-Spin columns simultaneously under vacuum (&ge;400 mm Hg). Linear polyethylene body, one-way Luer-Lock stopcocks, polypropylene vacuum connector. Compatible with most Zymo nucleic acid purification kits.

Capability

Compatibility

Composition

EZ-Vac96 Vacuum Manifold

EZ-Vac96™ Vacuum Manifold S7003 by Zymo Research — processes up to 96 samples simultaneously using vacuum-driven column flow, eliminating centrifugation. Compatible with ZymoPURE™ 96 Plasmid Miniprep Kit (D4214, D4215); requires vacuum pump capable of up to 300 mmHg and 6.5 mm ID tubing. Chemical-resistant construction with external catch flask. Order via <a href="https://www.mbpinc.net/quickorder">Quick Order</a> or contact <a href="mailto:customerservice@mbpinc.net">customerservice@mbpinc.net</a>.

Required Equipment

<h2>What are PCR and molecular assays for microbiomics?</h2>
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PCR and molecular assays in this category use quantitative PCR (qPCR) or digital PCR to measure the copy number of a defined DNA target, most often the 16S rRNA gene, to determine total bacterial load in a sample, or a specific pathogen or functional gene target for detection purposes. Unlike 16S or shotgun sequencing, which characterize the full taxonomic or functional composition of a community, these molecular assays provide a faster, more targeted quantitative or presence/absence readout for a specific question.
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<h2 dir="ltr">What you will discover:</h2>
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<ul>
<li dir="ltr" aria-level="1">
Femto&trade; Quantification Kits: Highly sensitive systems engineered for the detection of human, bacterial, or fungal DNA at the femtogram level with negligible sequence bias.
</li>
<li dir="ltr" aria-level="1">
High-Fidelity qPCR Premixes: Tailored master mixes designed for effective amplification and enhanced nuclear signal localization in low-biomass samples.
</li>
<li dir="ltr" aria-level="1">
Certified DNA Standards: Reference materials tested for reproducibility and No Template Controls (NTC) designed to calibrate the linear dynamic range and avert background contamination.
</li>
<li dir="ltr" aria-level="1">
ZymoTaq&trade; Specialized Polymerases: Enzymes that are heat-activated and free of nucleases, crafted to minimize non-specific amplification and guarantee high specificity in workflows associated with CRISPR.
</li>
</ul>
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<h2>How to choose PCR and molecular assays</h2>
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Use total bacterial load qPCR to screen samples before sequencing
A qPCR assay targeting the 16S rRNA gene quantifies total bacterial content in a sample, providing a useful pre-sequencing check for low-biomass samples likely to produce poor amplification or unreliable sequencing results if processed without this screening step.
Decide between qPCR and digital PCR based on sensitivity needs
Digital PCR can offer higher sensitivity and more accurate quantification than standard qPCR, particularly for low-biomass samples at the limit of detection, though at the cost of longer processing time, generally a meaningful tradeoff only when standard qPCR proves insufficient.
Confirm your qPCR assay design addresses known technical pitfalls
Well-designed 16S qPCR assays address known issues like self-priming or mispriming of unintended targets, amplification bias from non-optimal primer coverage, and amplicon size constraints for compatibility with clinical or high-throughput qPCR platforms.
Use pathogen-specific or functional gene qPCR for targeted detection
Beyond total bacterial load, qPCR can target a specific pathogen's single-copy gene or a functional gene of interest, such as an antibiotic resistance gene, providing a faster, more targeted answer than waiting for full sequencing and bioinformatic analysis.
Plan for known PCR limitations in environmental and clinical samples
Standard qPCR can be limited by reliance on standard reference materials for quantification and is prone to inhibition from substances naturally present in environmental or clinical samples, such as heavy metals or organic matter, which digital PCR can sometimes overcome with improved robustness.
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<h2>Specifications context</h2>
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A PCR-based total bacterial quantification assay can provide an exact calculation of bacterial abundance useful for assessing whether a sample is likely to yield positive amplification before committing it to full sequencing, helping avoid wasted sequencing runs on low-biomass samples. As of 2026, digital PCR continues to see increased adoption over standard qPCR specifically for low-biomass, environmental, or inhibitor-prone sample types, where its improved sensitivity and accuracy can outweigh its longer processing time.
<a href="https://mbpinc.net/contact-us">Reach out to the expert team at MBP Inc.</a> now to ask for a quote on the appropriate PCR and molecular assays for your laboratory.

PCR & Molecular Assays

Femto™ Bacterial DNA Quantification Kit (100 Rxns.)

E2006 by Zymo Research — Femto™ Bacterial DNA Quantification Kit, 100 reactions, qPCR detection 20 fg to 20 ng bacterial DNA from 1 µL sample. 16S rRNA primers; selective in mixed non-bacterial backgrounds. Store at −20°C.

Detection Range

Femto™ Bacterial qPCR Premix (1.8 ml)

Femto™ Bacterial qPCR Premix (E2006-1) by Zymo Research — 1.8 mL, 100 reactions, targets 16S rRNA gene, detects as few as 20 fg bacterial DNA (5 copies E. coli), 20 fg–20 ng quantification range. Includes bacterial DNA standards 1–7 and NTC.

Femto™ Fungal DNA Quantification Kit (100 Rxns.)

E2007 by Zymo Research is the Femto™ Fungal DNA Quantification Kit (100 rxns) — detects as little as 20 fg of fungal DNA per reaction using SYTO® 9 and ITS1-F/ITS2-R primers. Detection range 20 fg to 20 ng. S. cerevisiae-derived 7-point standard curve. High fungal specificity; no cross-reactivity with bacterial, plant, or animal DNA.

Femto™ Fungal qPCR Premix (1.8 ml)

E2007-1 by Zymo Research — Femto Fungal qPCR Premix; 1.8 mL 2× premix; ITS-targeting primers; 20 fg–20 ng detection range; ≥2 copies S. cerevisiae; compatible with any qPCR instrument; store at –20°C.

Femto™ Human DNA Quantification Kit (100 Rxns.)

E2005 by Zymo Research is the Femto™ Human DNA Quantification Kit (100 rxns) — detects as little as 20 femtograms of human DNA per reaction using SYTO® 9 and LINE-1 primers. Detection range 20 fg to 20 ng. HeLa-derived 7-point standard curve. High specificity; no cross-reactivity with non-human DNA.

Femto™ Human qPCR Premix (1.8 ml)

E2005-1 by Zymo Research: 1.8 ml 2× qPCR premix for human DNA quantification from 20 fg to 20 ng per reaction (&lt;1 copy of human genomic DNA). Targets LINE-1 on SYBR Green channel. Compatible with any real-time qPCR instrument. Store at −20°C.

<h2 data-section-id="v1drft" data-start="0" data-end="43">What are cloning chemicals and reagents?</h2>
&nbsp;
Cloning chemicals and reagents cover the enzymes, buffers, and molecular biology-grade chemicals used in DNA fragment preparation, modification, and purification within a cloning workflow, including restriction endonucleases, T4 DNA ligase and other DNA-modifying enzymes (phosphatases, polymerases), reaction buffers, and plasmid extraction reagents. Related entities include restriction enzyme digestion, DNA dephosphorylation/phosphorylation, plasmid DNA purification (column-based and magnetic bead-based), and enzyme unit definitions.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Targeted XJa and XJb strains for faster recovery of proteins.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Mix &amp; Go! solutions for optimized and dependable bacterial transformation.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Culture Media &amp; Supplements used for yeast research, and include YPD Plus and mating pheromones.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Extraction and Lysis Reagents include reliable genomic preparation and yeast protein kits.</li>
<li dir="ltr" style="font-family: arial, helvetica, sans-serif;" role="presentation">Chromogenic Substrates and Enzymatic Inducers with highly pure X-GAL and IPTG for cloning and blue-white screening.</li>
</ul>
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<h2 data-section-id="1daajgc" data-start="866" data-end="913">How to choose cloning chemicals and reagents</h2>
&nbsp;
Restriction enzyme selection and buffer compatibility
Restriction enzymes require specific reaction buffers, and many modern enzyme lines use a single universal buffer compatible across multiple enzymes to simplify double-digest reactions; confirm buffer compatibility when combining enzymes from different suppliers or using older single-buffer-per-enzyme formulations.
Enzyme unit definitions and reaction scale
Restriction enzyme and ligase activity is defined in units per microliter, with one unit typically defined as the amount needed to digest or ligate a defined quantity of standard substrate DNA under specified conditions in a set time; scale enzyme quantity to the amount of DNA being processed rather than assuming a fixed volume works for all reaction sizes.
Plasmid purification grade
Plasmid DNA extraction reagents range from molecular biology grade, suitable for general cloning and sequencing, to transfection-grade or endotoxin-free formulations required for applications such as lentiviral packaging or mammalian cell transfection, where endotoxin contamination can reduce transfection efficiency or cause cell stress.
Dephosphorylation for preventing vector self-ligation
Alkaline phosphatase treatment of a linearized vector before ligation removes 5' phosphate groups, preventing vector self-ligation and improving the ratio of recombinant clones; this step is particularly useful when the vector and insert share compatible sticky ends that could otherwise religate without insert incorporation.
&nbsp;
<h2 data-section-id="1fljvas" data-start="3459" data-end="3484">Specifications context</h2>
&nbsp;
Restriction enzymes and ligases are supplied at defined unit concentrations (commonly 10&ndash;20 units per microliter for restriction enzymes), with reaction buffers formulated for specific pH and salt conditions optimized for enzyme activity. Plasmid purification kits are differentiated by yield (micrograms of DNA recovered), purity (A260/A280 ratio), and endotoxin level (endotoxin units per microgram), with endotoxin-free kits specifying levels below a defined threshold suitable for transfection applications.&nbsp;
This sub-category is part of MBP's cloning catalog alongside ligation independent cloning kits and transformation kits and competent cells, used downstream of enzyme-based fragment preparation. Labs producing custom lentivirus for immortalization can also review MBP's cell immortalization catalog. MBP's specialist team can help confirm enzyme buffer compatibility and plasmid purification grade for a specific downstream application before order placement.
<a href="https://mbpinc.net/contact-us">Contact the expert team </a>at MBP today to request a quote for high-purity chemicals and reagents.

Chemicals/Reagents

Frozen-EZ Yeast Solution

Frozen-EZ Yeast Transformation II solution components by Zymo Research — ZYM-T2002 (Solution I, 60 ml), ZYM-T2003 (Solution II, 6 ml), and ZYM-T2004 (Solution III, 60 ml) — are the individual buffer components of the Frozen-EZ Yeast Transformation II system. Compatible with S. cerevisiae, C. albicans, S. pombe, and Pichia pastoris. Stored at 0–4°C; sold separately for independent replenishment of any depleted solution.