Zymo Reagents

<h2>What are PCR Cleanup Kits?</h2>
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PCR cleanup kits remove residual PCR reaction components -- primers (&lt;100 bp), primer dimers, unincorporated dNTPs, DNA polymerase, buffer salts, and mineral oil - from PCR amplification products using silica-membrane spin columns and a bind-wash-elute protocol. The purified PCR amplicon (&gt;=100 bp) is recovered in 20-50 ul of water or elution buffer, free of inhibitors that would interfere with downstream steps, including Sanger sequencing, restriction enzyme digestion, ligation, NGS library preparation, and in vitro transcription. The procedure takes 5-10 minutes using a standard microcentrifuge with no organic solvents, precipitation, or centrifugation spins beyond the bind/wash/elute steps. Use a PCR cleanup kit immediately after PCR whenever the downstream application requires an inhibitor-free amplicon - primers and excess dNTPs left in the reaction will reduce sequencing quality, compete in ligation reactions, and inflate NGS background noise.
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<h2 dir="ltr">What you will find:</h2>
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Oligo Clean &amp; Concentrator: Precisely designed systems for the quick retrieval of single-stranded DNA, RNA, and oligonucleotides from enzymatic processes.
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OneStep&trade; PCR Inhibitor Removal: Tailored columns and 96-well formats engineered to eliminate polyphenols, humic acids, and lipids that hinder PCR kinetics.
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ssDNA/RNA Clean &amp; Concentrator&trade;: An adaptable method for purifying and concentrating small nucleic acid segments, ensuring isoform specificity.
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ZR-96 High-Throughput Systems: Scalable formats of 96-well plates designed for automated lab processes, guaranteeing reproducibility-validated outcomes across extensive sample groups.
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<h2>How to Choose a PCR Cleanup Kit</h2>
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Binding Capacity
Standard PCR cleanup columns bind up to 5-25 ug of DNA, depending on the kit; 25 ug capacity (Thermo Fisher GeneJET) accommodates typical preparative PCR reactions. For high-yield PCR reactions producing &gt;25 ug of amplicon, split the reaction across two columns and pool the eluates, or use a higher-capacity kit format.
Fragment Size Range
Standard PCR cleanup kits retain fragments &gt;=100 bp and discard everything shorter. For amplicons between 70 and 100 bp (e.g., short RT-qPCR products or miRNA amplicons), use a kit with an extended lower size limit -- the Thermo Fisher GeneJET kit retains fragments from 25 bp to 20 kb, covering this range. For amplicons shorter than 25 bp, conventional silica-column cleanup will not work; use gel purification or size-selective bead cleanup (e.g., AMPure XP at adjusted bead ratios).
Minimum Elution Volume
If the downstream application requires a high DNA concentration (Sanger sequencing needs &gt;20 ng/ul input), select a kit that elutes in as little as 20-25 ul without significant yield loss.&nbsp;
pH Indicator
Kits include a pH indicator dye in the binding buffer that turns yellow when the pH is correct for DNA binding and remains orange/red if the pH is too high (causing DNA loss). This is useful when purifying PCR products amplified in high-pH buffers. Kits without pH indicators require careful attention to binding buffer volume ratios to ensure efficient DNA adsorption.
96-Well Throughput
For screening workflows producing multiple amplicons per sample, use 96-well PCR purification plates with vacuum manifolds for simultaneous processing of all 96 wells. 96-well formats are essential for high-throughput genotyping and sequencing library preparation pipelines.
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<h2>Specifications Context</h2>
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Key benchmarks for PCR cleanup kits: &gt;=70% DNA recovery for fragments 100 bp-10 kb, A260/A280 &gt;= 1.7 in eluate, complete removal of primers and dNTPs (confirmed by capillary electrophoresis with no peaks below 100 bp), and elution in &lt;=50 ul of water or TE. The Thermo Scientific GeneJET PCR Purification Kit specifies recovery rates up to 100% with a binding capacity of 25 ug per column in a 5-minute protocol. AAT Bioquest study comparing commercial PCR cleanup kit performance confirmed that silica-column kits consistently achieve primer and dimer removal equivalent to ethanol precipitation with significantly reduced protocol time. PCR cleanup is a mandatory step before NGS library preparation in nearly all sequencing-based workflows at institutions, including Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center, where primer and dimer contamination in libraries produces low-complexity sequencing reads that reduce effective coverage.
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Purify your amplicons and remove reaction noise&mdash;<a href="https://mbpinc.net/contact-us">reach out to MBP Inc.</a> now to obtain a quote for your PCR cleanup process.

PCR Cleanup Kits

MSDS - D7010-1

MSDS- 7010-2

MSDS - 7010-3

MSDS - D7010

ssDNA/RNA Clean & Concentrator™

The D7010 by Zymo Research is a 20-prep single-stranded DNA/RNA cleanup kit that selectively purifies ssDNA and ssRNA fragments of 17–200 nucleotides from double-stranded contaminants in approximately 10 minutes, yielding up to 10 µg per prep at A260/280 &gt; 1.8 from a minimum 6 µl elution volume. Compatible with PCR, RT-qPCR, hybridization, and NGS workflows.

Equipment

Purity

Sample Source

Size Range

Yield

Manufacturer

Shipping Condition

Storage Condition

ssDNA/RNA Clean & Concentrator™ (20 Preps.)

DNA/RNA Binding Buffer (10 ml)

DNA/RNA Binding Buffer (25 ml)

DNA/RNA Binding Buffer (50 ml)

DNA/RNA Prep Buffer (10 ml)

DNA/RNA Prep Buffer (200 ml)

DNA/RNA Prep Buffer (25 ml)

DNA/RNA Prep Buffer (50 ml)

DNA/RNA Wash Buffer (Concentrate) (12 ml)

DNA/RNA Wash Buffer (Concentrate) (24 ml)

DNA/RNA Wash Buffer (Concentrate) (6 ml)

ssDNA/RNA Clean & Concentrator™ (50 Preps.)

<h2>What are Spin-Column Plant RNA Extraction Kits?</h2>
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Spin-column plant RNA extraction kits purify total RNA from plant tissue - leaves, stems, roots, buds, flowers, fruit, and seeds - using a liquid nitrogen grinding or bead-beating disruption step followed by a dual-column silica-membrane workflow in a standard microcentrifuge. The Zymo Quick-RNA Plant Miniprep Kit uses a Zymo-Spin IIICG column to physically retain and discard genomic DNA while RNA passes through into the collection tube, then a Zymo-Spin IIC column to bind, wash, and elute total RNA including small RNAs &gt;=17 nt. The full protocol takes 20-30 minutes per batch of 1-12 samples and yields up to 50 ug RNA per extraction. Use the spin-column plant RNA format for routine lab use processing 1-24 plant tissue samples per day without automation infrastructure, or when your samples require a fast, phenol-free extraction workflow validated for standard crop and model plant species.
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<h2 dir="ltr">What you will find:</h2>
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<ul>
<li data-section-id="1ds2uf1" data-start="25" data-end="79">Recovery of ultra-pure total RNA from plant tissues.</li>
<li data-section-id="1n1wgzn" data-start="80" data-end="148">Effective processing of tough and difficult-to-lyse plant samples.</li>
<li data-section-id="197xy8o" data-start="149" data-end="210">Rapid RNA purification using silica spin-column technology.</li>
<li data-section-id="te47gz" data-start="211" data-end="257">Organic solvent-free RNA isolation workflow.</li>
<li data-section-id="1ru7scj" data-start="258" data-end="332" data-is-last-node="">High-quality RNA suitable for downstream molecular biology applications.</li>
</ul>
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<h2>How to Choose a Spin-Column Plant RNA Kit</h2>
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Tissue Type and Inhibitor Load
Soft, low-polyphenol tissues (Arabidopsis leaves, tobacco, rice leaves) extract cleanly with guanidinium-based spin-column kits. Fibrous, woody, or high-polyphenol tissues (mature stems, bark, fruit peel, seeds) require either CTAB-based upstream lysis followed by column purification, or additional grinding in liquid nitrogen to achieve complete disruption before adding lysis buffer.
CTAB Compatibility
Confirm the spin-column kit is compatible with CTAB-based pre-lysis if you work with polyphenol-rich species. Zymo Direct-zol RNA Miniprep Plus is confirmed compatible with CTAB-extracted samples from Pinus and Geranium; the lysis protocol for CTAB-compatible extraction is available from Zymo Research as a supplementary protocol.
Two-Column DNA Depletion vs. On-Column DNase
The two-column Zymo-Spin IIICG/IIC architecture provides physical gDNA depletion without a separate DNase incubation, saving 15 minutes per batch. For RNA-seq applications where any gDNA mapping artefacts must be eliminated, add optional on-column DNase I treatment after the IIICG column step. Plant genomes contain repetitive sequences that can map to cDNA targets; gDNA-free RNA is essential for accurate intron-spanning transcript quantification.
Inhibitor Removal Filter
Use Zymo-Spin III-HRC Spin Filters on the eluted RNA when A260/A230 &lt; 1.5, or when you know the tissue type is high in polysaccharides (starch-rich seeds, high-pectin fruit) or polyphenols. Each filter reduces the yield by 10-20% but substantially improves RT-qPCR amplification efficiency.
Elution Strategy
For RNA-seq: elute in 50-100 ul and quantify by Qubit RNA HS Assay for accurate low-concentration measurement. For RT-qPCR only: elute in 25-30 ul to concentrate RNA and reduce the volume needed per reaction well.
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<h2>Specifications Context</h2>
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Quality benchmarks for spin-column plant RNA: A260/A280 &gt;= 1.8-2.0 (typical for plant RNA due to low protein content relative to total RNA), A260/A230 &gt;= 1.5 (target &gt;= 1.8 for RNA-seq), and RIN &gt;= 7 from well-processed fresh tissue. The Zymo Quick-RNA Plant Miniprep Kit achieves A260/A280 &gt; 1.8 and A260/A230 &gt; 1.8 for standard model plant species under its standard protocol. As of 2025, Arabidopsis thaliana and rice remain the most intensively studied model plant species; published plant RNA-seq methods from labs at institutions including the Howard Hughes Medical Institute and Vanderbilt University have validated spin-column plant RNA kits for transcriptome-wide expression profiling. For high-polyphenol crop species, including grapevine, citrus, and coffee, contact MBP's technical team for CTAB-compatible protocol guidance.
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<a href="https://mbpinc.net/contact-us">Contact the expert team at MBP Inc.</a> today and get high-quality spin-column systems for your advanced botanical research.

Spin-column

Quick-RNA™ Plant Miniprep Kit (50 Preps.)

Isolate inhibitor-free RNA from plant and seed samples.

<h2>What are methylated dNTPs?</h2>
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Methylated dNTPs are base-modified deoxynucleotide analogs, the most important being 5-methyl-dCTP (2'-deoxy-5-methylcytidine 5'-triphosphate), in which the cytosine base carries a methyl group at the carbon-5 position. This is the same position methylated in naturally occurring genomic 5-methylcytosine, the primary DNA methylation mark studied in epigenetics research. Substituting 5-methyl-dCTP for standard dCTP in a PCR reaction or in vitro synthesis produces a defined, fully cytosine-methylated DNA template from a known sequence.
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<h2 dir="ltr">What you will find:</h2>
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5-Methyl dCTP (10 mM) (100 &micro;l): for high-purity enzymatic incorporation into methylated DNA strands.
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5-Methylcytosine dNTP Mix (10 mM) (250 &micro;l): pre-validated nucleotide blends for controlled epigenetic assay workflows.
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<h2>How to use methylated dNTPs</h2>
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Substitute 5-methyl-dCTP for dCTP in PCR to synthesize defined methylated DNA
A PCR reaction using 5-methyl-dCTP in place of standard dCTP produces a fully methylated amplicon in which every cytosine carries the 5-methyl modification, providing a positive control with a known and consistent methylation status distinct from the partial, variable methylation of a genomic DNA control.
Use methylated DNA as a positive control for bisulfite or enzymatic conversion workflows
Running 5-methyl-dCTP-synthesized fully methylated DNA through your bisulfite or enzymatic conversion protocol confirms the method correctly preserves methylated cytosines while converting unmethylated ones, catching conversion efficiency problems at the control stage before they affect interpretation of real samples.
Test methylation-sensitive restriction enzymes using 5-methyl-dCTP-produced substrates
Some restriction enzymes cut methylated sequences while others are inhibited by methylation at their recognition site, and a PCR-synthesized, fully methylated substrate of known sequence provides a clean, defined test of whether a specific enzyme is methylation-sensitive or methylation-dependent.
Use as an in vitro substrate for TET enzyme oxidation studies
Since 5-methylcytosine is the starting substrate for TET family enzyme oxidation into 5-hydroxymethylcytosine and further products, fully methylated DNA synthesized with 5-methyl-dCTP provides a defined, homogeneous substrate for in vitro TET enzyme activity assays.
Store methylated dNTPs appropriately to maintain activity
Methylated dNTP analogs are generally stored at -20&deg;C, similar to standard dNTPs, with short-term exposure to ambient temperature acceptable but prolonged room-temperature storage avoided to prevent hydrolysis of the phosphate groups.
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<h2>Specifications context</h2>
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5-methyl-dCTP is typically supplied as a 10 mM solution at pH 7.0 and can be diluted using sterile distilled water or TE buffer, and it can be used in PCR, RT-PCR, and other DNA synthesis applications at the same concentration as standard dCTP in a reaction mix, with 5-methylated DNA probes made this way serving as methylation reference fragments or as pull-down substrates for 5-hydroxymethylcytosine-binding proteins. As of 2026, 5-methyl-dCTP-synthesized control DNA remains a standard tool in epigenetics research labs specifically because it provides a modification-defined substrate without relying on the variable or partially characterized methylation patterns of genomic positive controls.
<a href="https://mbpinc.net/contact-us">Contact the expert team at MBP</a> and get high-quality methylated (dNTPs) for your lab.

Methylated

5-Methylcytosine dNTP Mix (10 mM) (250 µl)

dNTP mixture containing the modified deoxynucleotide 5-mC for use with PCR, mass spec, etc.

Applicable For 

Concentration

Sample Storage

<h2>What are ChIP buffers?</h2>
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ChIP buffers are the aqueous formulations used at each stage of a chromatin immunoprecipitation protocol: cell lysis buffer disrupts the plasma membrane and releases nuclear content, nuclear lysis buffer solubilizes chromatin under conditions compatible with subsequent immunoprecipitation, sonication buffer maintains chromatin stability during shearing, ChIP dilution buffer reduces SDS concentration from the lysis buffer to allow antibody-antigen binding, sequential wash buffers with increasing ionic strength and detergent remove non-specifically bound chromatin while preserving the specific antibody-antigen-DNA complex, and elution buffer releases the captured complex from the antibody-bead resin before de-crosslinking.
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<h2 dir="ltr">What you will find:</h2>
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<ul>
<li dir="ltr" role="presentation">MN Digestion Buffer used in MNase-based workflows for enzymatic fragmentation of&nbsp; chromatin&nbsp;</li>
<li dir="ltr" role="presentation">Chromatin Shearing Buffer using sonification for chromatin disruption and preparation</li>
<li dir="ltr" role="presentation">5X MN Stop Buffer for the termination of enzymatic digestion reactions</li>
<li dir="ltr" role="presentation">Chromatin Dilution Buffer used in ChIP assays to provide optimized conditions for antibody binding&nbsp;</li>
<li dir="ltr" role="presentation">Chromatin Wash Buffer I, II, and III for background reduction and step-by-step non-specific binding removal&nbsp;</li>
<li dir="ltr" role="presentation">ChIP DNA Binding Buffer for purification and capture of immunoprecipitated DNA</li>
<li dir="ltr" role="presentation">5X Chromatin Elution Buffer for protein&ndash;DNA complexes recovery</li>
<li dir="ltr" role="presentation">5M NaCl for enhancing elution and chromatin stabilization</li>
<li dir="ltr" role="presentation">Nuclei Prep Buffer used before chromatin extraction for superior nuclear isolation</li>
</ul>
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<h2>How to use ChIP buffers</h2>
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Always add protease inhibitors to lysis and wash buffers immediately before use
Protease inhibitors must be added fresh to cell lysis and nuclear lysis buffers immediately before use, since most inhibitors are unstable in aqueous solution and lose activity quickly, and without them, nuclear proteases released during lysis will degrade histone tails and reduce ChIP enrichment of histone modifications.
Confirm SDS concentration is diluted before immunoprecipitation
High SDS in the nuclear lysis buffer is necessary for chromatin solubilization and sonication, but must be diluted approximately 10-fold using ChIP dilution buffer before antibody addition, since high SDS disrupts antibody-antigen binding and reduces immunoprecipitation efficiency.
Keep all buffers and chromatin on ice throughout the workflow after lysis
Chromatin prepared for ChIP is sensitive to non-specific interactions and protease activity after cell lysis, and maintaining samples at 4&deg;C throughout all lysis, sonication, immunoprecipitation, and wash steps minimizes these effects and preserves specificity of the enrichment.
Optimize wash buffer stringency to balance specificity against yield
ChIP wash buffers are applied sequentially at increasing ionic strength and detergent concentration to remove non-specifically bound chromatin; conditions too stringent can also strip the specific antibody-antigen-DNA complex from the beads, reducing yield, so optimization of wash conditions for each antibody-target combination improves performance.
Confirm elution buffer composition fits your downstream application
Standard ChIP elution buffers containing SDS and sodium bicarbonate release the protein-DNA complex and reverse crosslinks, but high SDS in the eluate can inhibit some NGS library preparation enzymes, making a DNA cleanup step after elution important before proceeding to library prep.
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<h2>Specifications context</h2>
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Protease inhibitor cocktails, added fresh to lysis buffers immediately before ChIP, are a standard component across kit formats and in-house protocols, since even brief protease activity can compromise histone modification detection by degrading the histone tails that ChIP antibodies recognize. As of 2026, ChIP buffer formulations compatible with low-input chromatin and NGS library preparation continue to be optimized for primary cell and tissue ChIP workflows.
<a href="https://mbpinc.net/contact-us">Contact the expert team </a>at MBP and request a quote today to get high-quality ChIP buffers for your lab.

Buffers

Chromatin Wash Buffer III (30 ml)

Chromatin Wash Buffer III (D5210-5-30) by Zymo Research is a 30 ml wash reagent for the third sequential wash step in Zymo-Spin ChIP Kit (D5209, D5210) protocols, removing residual non-specific binding from Protein A bead/antibody/chromatin complexes before DNA elution. Sold separately for kit replenishment or standalone use; store at room temperature. MBP is a registered vendor for Howard Hughes Medical Institute, Vanderbilt University, MD Anderson Cancer Center, Eurofins, and many other institutes across the USA.

United States

Texas

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