Zymo Research

<h2>What Are Zymo Research Buffers?</h2>
Zymo Research buffers are formulation-specific reagents used at defined steps &mdash; lysis, binding, wash, and elution &mdash; in Zymo-Spin column-based purification protocols for DNA, RNA, and bisulfite-converted DNA. Each buffer is optimized for a specific kit family: DNA Wash Buffer concentrate (requires ethanol addition before use) removes salts and contaminants before elution from Zymo-Spin silica columns; DNA Elution Buffer (10 mM Tris, pH 8.5, 0.1 mM EDTA) releases purified DNA from the matrix; RNA Wash Buffer supports RNA extraction kits including Quick-RNA and Direct-zol lines; M-Elution Buffer is designed for eluting bisulfite-converted DNA in EZ DNA Methylation kits. Researchers typically order these separately when a single buffer component runs out before the rest of the kit, or when scaling up a protocol beyond the volume included.
TL;DR: Order Zymo buffers individually to replenish a specific step in your existing Zymo workflow without replacing the full kit.
<h2>How to Choose Zymo Research Buffers</h2>
<h3>Match the buffer to your kit family</h3>
Every Zymo buffer is paired to a specific kit line. DNA Wash Buffer and DNA/RNA Wash Buffer concentrate are used in DNA Clean &amp; Concentrator, Quick-DNA, and Zymoclean Gel DNA Recovery kits. RNA Wash Buffer pairs with Quick-RNA kits. ZymoBIOMICS DNA Wash Buffer 1 and Wash Buffer 2 are specific to the ZymoBIOMICS microbiomics line. Substituting a buffer from a different kit family can compromise yield or purity.
<h3>Confirm ethanol addition requirements before use</h3>
Several Zymo wash buffer concentrates require addition of 96-100% ethanol to the bottle before first use &mdash; the label states the exact volume. DNA Wash Buffer concentrate, DNA/RNA Wash Buffer concentrate, and Urine DNA Wash Buffer concentrate all require this step. Pre-made (non-concentrate) versions such as RNA Wash Buffer are supplied ready to use.
<h3>Select the right volume for your throughput</h3>
Zymo buffers are available in sizes from 6 ml (single-experiment replenishment) up to 500 ml (Buffer P1 Red, for high-volume plasmid prep labs). For labs processing more than 50 samples per week, ordering the largest available size reduces per-sample cost and the frequency of reordering.
<h3>Choose elution buffer chemistry based on downstream application</h3>
DNA Elution Buffer (10 mM Tris pH 8.5, 0.1 mM EDTA) is the standard for most PCR and sequencing applications. For applications sensitive to EDTA &mdash; such as some restriction enzyme digests or direct use with divalent cation-dependent enzymes &mdash; eluting in molecular-grade water or a Tris-only buffer is preferable. M-Elution Buffer is specifically formulated for bisulfite-converted DNA and should not be substituted with standard elution buffer in methylation workflows.
<h3>Verify research-use-only status</h3>
All Zymo Research buffers sold through MBP are for research use only (RUO). They are not cleared for in vitro diagnostic use. For clinical or diagnostic laboratory applications, confirm regulatory status with your institutional compliance officer before use.
<h2>Compare Zymo Buffer Types</h2>
<table>
<thead>
<tr>
<th>Buffer Type</th>
<th>Primary Application</th>
<th>Kit Family</th>
<th>Format Available</th>
</tr>
</thead>
<tbody>
<tr>
<td>DNA Wash Buffer (concentrate)</td>
<td>Salt removal before DNA elution</td>
<td>DNA Clean &amp; Concentrator, Quick-DNA</td>
<td>6 ml &ndash; 200 ml</td>
</tr>
<tr>
<td>DNA/RNA Wash Buffer (concentrate)</td>
<td>Salt removal for dual DNA/RNA preps</td>
<td>Quick-DNA/RNA kits</td>
<td>6 ml &ndash; 200 ml</td>
</tr>
<tr>
<td>DNA Elution Buffer (10 mM Tris pH 8.5, 0.1 mM EDTA)</td>
<td>DNA release from silica column</td>
<td>All Zymo DNA purification</td>
<td>16 ml &ndash; available sizes vary</td>
</tr>
<tr>
<td>RNA Wash Buffer</td>
<td>RNA purification wash step</td>
<td>Quick-RNA kits</td>
<td>Ready-to-use</td>
</tr>
<tr>
<td>M-Elution Buffer</td>
<td>Elution of bisulfite-converted DNA</td>
<td>EZ DNA Methylation kit families</td>
<td>Small volume</td>
</tr>
<tr>
<td>ZymoBIOMICS DNA Wash Buffer 2</td>
<td>Metagenomic/microbiomic DNA cleanup</td>
<td>ZymoBIOMICS DNA kits</td>
<td>Sold separately</td>
</tr>
<tr>
<td>Buffer P1 Red</td>
<td>Alkaline lysis resuspension (plasmid prep)</td>
<td>Zyppy Plasmid Miniprep</td>
<td>10 ml &ndash; 500 ml</td>
</tr>
</tbody>
</table>
<h2>Specifications Context</h2>
Zymo wash buffer concentrates are supplied at a defined fold-concentration (commonly 4x or 6x) and require ethanol addition to reach working strength &mdash; the exact ratio is printed on the bottle and in the kit protocol. Elution buffer volumes for Zymo-Spin columns typically range from 6 to 100 &micro;l per elution; larger elution volumes improve total yield at the cost of DNA concentration. For DNA elution from Zymo-Spin columns, the protocol recommends a minimum 1-minute contact time between elution buffer and the silica matrix to maximize recovery of fragments 10 kb and above. As of 2025, Zymo Research tests all buffer lots for performance consistency, with integrity guaranteed for up to one year from purchase date.
Browse the full <a href="https://www.notion.so/reagents">Zymo Research reagents collection at MBP</a> for kits and columns that use these buffers, or visit our <a href="https://www.notion.so/reagents/buffers">reagent buffers category</a> for non-Zymo buffer options including ABM and other brands. For volume orders or purchase orders, use the <a href="https://www.notion.so/quickorder">Quick Order</a> tool or <a href="https://www.notion.so/contact-us">contact us</a> directly &mdash; MBP is a registered vendor for institutional procurement systems.
Last updated: June 2025
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Zymo Buffers

MSDS

RNA Recovery Buffer (10 ml)

RNA Recovery Buffer R1070-1-10 by Zymo Research is a 10 mL elution buffer used in the Quick-cfRNA™ Serum &amp; Plasma Kit (R1059) to recover RNA from the Spin-Away™ filter column. Used at 200 µL per prep; stored at room temperature. Available as a standalone replacement component.

Manufacturer

Shipping Condition

Storage Condition

<h2>What Are Nucleases?</h2>
&nbsp;
Nucleases are enzymes that cleave phosphodiester bonds between nucleotide subunits in nucleic acids. Deoxyribonucleases (DNases) act on DNA; ribonucleases (RNases) act on RNA; and some nucleases (S1 Nuclease, Mung Bean Nuclease) act on both single-stranded DNA and RNA. Nucleases are further divided into endonucleases, which cleave internal phosphodiester bonds, and exonucleases, which progressively remove nucleotides from the 5' or 3' terminus of a strand. Major research nucleases include DNase I (non-specific endonuclease for both ss- and ds-DNA), RNase A (cleaves single-stranded RNA at pyrimidine residues), RNase H (degrades the RNA strand of RNA: DNA hybrids), Exonuclease III (removes nucleotides from 3'-recessed or blunt ends of duplex DNA), S1 Nuclease (degrades single-stranded DNA or RNA), and RNase R (degrades linear RNA but not circular RNA). Match the nuclease to the substrate type (single-stranded vs. double-stranded, DNA vs. RNA), the directionality required (endo vs. exo), and cofactor compatibility with your reaction buffer.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" aria-level="1">
PureRec RNase A (Recombinant): A ribonuclease free of animal-derived components, designed for the swift elimination of RNA from DNA samples, ensuring no threat of viral contamination.
</li>
<li dir="ltr" aria-level="1">
DNase I Set (RNase-free): A highly effective endonuclease formulated for complete DNA digestion in delicate RNA applications while preserving the integrity of the transcript.
</li>
<li dir="ltr" aria-level="1">
PureRec Duplex-Specific Nuclease (DSN): A unique enzyme designed to equalize high-abundance transcripts, greatly enhancing the identification of rare variants in cDNA libraries.
</li>
<li dir="ltr" aria-level="1">
RNase R: A distinctive 3'-to-5' exoribonuclease that breaks down linear RNA but preserves circular RNA forms, crucial for the identification of circRNA.
</li>
<li dir="ltr" aria-level="1">
RNaseOFF Inhibitor: A strong protein-based barrier that counteracts a wide range of RNases, maintaining the delicate transcriptional environment of your samples.
</li>
</ul>
&nbsp;
<h2>How to Choose Nucleases</h2>
&nbsp;
DNase selection
DNase I (bovine pancreatic, recombinant) non-specifically cleaves both single- and double-stranded DNA in the presence of Mg2+ (random cleavage) or Mn2+ (double-strand cuts at approximately the same position on both strands). Use RNase-free DNase I for RNA preparations to remove genomic DNA contamination. Use Plasmid-Safe ATP-Dependent DNase to selectively degrade linear double-stranded DNA while preserving supercoiled and relaxed circular plasmid DNA. Baseline-ZERO DNase is optimized for the complete removal of trace DNA without damaging RNA.
RNase selection
RNase A cleaves single-stranded RNA at pyrimidine (C and U) residues to produce 3'-pyrimidine nucleotides; it is used to remove RNA from DNA preps, to perform RNase protection assays, and to analyze RNA secondary structure. RNase H degrades the RNA strand of RNA: DNA duplexes and is used after first-strand cDNA synthesis to remove the mRNA template. RNase R (3'-&gt;5' exoribonuclease) degrades all linear RNA without affecting circular RNA, and is used in circular RNA enrichment workflows and to characterize circular RNA splice junctions. Terminator 5'-Phosphate-Dependent Exonuclease (Terminator) digests linear RNA with a 5'-monophosphate, enriching for capped mRNA or circular RNA.
Exonuclease selection
Exonuclease III (Exo III) removes nucleotides from the 3' terminus of duplex DNA and generates single-stranded regions used in unidirectional nested deletions, mapping regulatory elements, and generating single-stranded templates for sequencing. Exonuclease I (Exo I) digests single-stranded DNA in the 3'-&gt;5' direction and is used after PCR to remove unincorporated primers before Sanger sequencing. Lambda Exonuclease removes nucleotides from 5'-phosphorylated duplex DNA in the 5'-&gt;3' direction and is used in isothermal amplification and strand displacement workflows.
Cofactor and inhibitor sensitivity
DNase I requires Mg2+ or Ca2+ for activity and is completely inhibited by EDTA at a 5 mM concentration. RNase A is active across a wide pH range (optimum 7.0-7.5) and is exceptionally stable; inactivation requires proteinase K digestion, phenol-chloroform extraction, or RNase inhibitor protein. RNase H requires Mg2+; RNase R requires Mg2+ and is most active between 37-50 degrees C.
Purity and application grade
For RNA-focused applications, all nucleases used on DNA substrates must be certified RNase-free. For DNA-focused work, DNase-free grades of RNases are required. Confirm lot-specific QC contamination data from the manufacturer before use in sensitive workflows.
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<h2>Specifications Context</h2>
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DNase I activity is expressed in Kunitz units: 1 unit increases A260 by 0.001 per minute per mL during DNA hydrolysis at pH 5.0. RNase A activity is expressed as the amount of enzyme hydrolyzing 50% of an RNA substrate under defined conditions; it remains active at a wide range of temperatures and is notoriously difficult to inactivate (requires boiling in SDS, proteinase K digestion, or phenol-chloroform extraction). RNase R from E. coli degrades linear RNA processively in the 3'-&gt;5' direction and is used at 2-10 U per microgram of total RNA to enrich for circular RNA species. RNase R treatment before library construction is the standard method for circular RNA sequencing (circRNA-seq) workflows on both short-read and long-read platforms. For protecting RNA from RNase contamination during nuclease-adjacent workflows, see&nbsp;<a href="https://mbpinc.net/reagents/molecular-biology/enzymes-and-inhibitors">RNase inhibitors</a>&nbsp;in the parent Enzymes and Inhibitors category.
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Safeguard your molecular images&mdash;<a href="https://mbpinc.net/contact-us">reach out to the MBP team</a> now to obtain a quote for our sophisticated nucleases and inhibitors.

Nucleases

Protocol

RNase A (30 mg)

RNase A (30 mg) (E1008-30) by Zymo Research — lyophilized, DNase-free, protease-free bovine pancreas RNase A, reconstitutable to 10 mg/ml. Thermostable; cleaves single-stranded RNA at 3' pyrimidine residues for RNA removal in DNA/plasmid purification workflows.

<h2>What are epigenetics NGS library preparation kits?</h2>
&nbsp;
Epigenetics NGS library preparation kits convert the DNA output of an upstream epigenetics workflow into an indexed sequencing library: adapters are ligated to the ends of each DNA fragment, an optional amplification step increases the total amount of library, and indexes are added to allow multiplexed sequencing of many samples in a single run. These kits are specifically optimized for epigenetics-specific inputs, including ChIP-enriched DNA (often low-yield, sheared to 200&ndash;750 bp), chromatin-accessible DNA from ATAC-seq (also low-yield and fragmented), and bisulfite-converted DNA (fragmented and chemically modified, with low-complexity sequence).
&nbsp;
<h2 dir="ltr">What You Will Discover:</h2>
&nbsp;
<ul>
<li dir="ltr">Groundbreaking single-tube processes that integrate bisulfite conversion and library preparation to chart entire genomes with extremely low input needs.</li>
<li dir="ltr">Rapid, efficient transposase-driven methods that seize open chromatin areas and dynamic regulatory environments in only a few hours.</li>
<li dir="ltr">Enzymatic restriction methods combined with targeted sequencing for affordable, high-density CpG coverage without incurring full-genome expenses.</li>
<li dir="ltr">Advanced multi-adapter ligation techniques designed to reduce bias and optimize library retrieval from fragmented or challenging DNA sources.</li>
<li dir="ltr">Post-bisulfite library preparation systems designed explicitly for sub-nanogram DNA quantities, individual cells, or extensively degraded specimens.</li>
<li dir="ltr">Locus-specific, genome-wide enrichment approaches aimed at accurately monitoring and characterizing 5-hydroxymethylcytosine alterations throughout the genome.</li>
</ul>
&nbsp;
<h2>How to choose epigenetics NGS library preparation kits</h2>
&nbsp;
Match your library prep kit to your specific epigenetics input type
ChIP-seq library prep kits are optimized for low-yield sheared chromatin enriched by immunoprecipitation, while ATAC-seq kits work with tagmented open chromatin fragments, and bisulfite or enzymatic methyl-seq library prep kits are specifically formulated for the highly fragmented, low-complexity sequence characteristics of bisulfite-converted DNA input.
Confirm the kit supports your input DNA amount
ChIP experiments, especially those targeting low-abundance transcription factors or run from limited cell numbers, often yield very little enriched DNA, and kits validated for low-input or picogram-scale library preparation are necessary to generate libraries with sufficient complexity without excessive PCR amplification introducing duplicates.
Choose an indexing strategy appropriate to your sample multiplexing plan
Dual-index strategies, using unique combinations of two distinct index sequences per sample, provide more reliable sample demultiplexing in highly multiplexed runs compared with single-index strategies, and confirming whether your kit supports the number of samples and multiplexing depth required is an important selection criterion.
Understand the impact of PCR cycles on library complexity and duplicate rate
Fewer PCR amplification cycles reduce the proportion of duplicate reads in sequencing data, which is especially important for low-complexity epigenetics libraries where overamplification can dominate output with copies of the same original fragment. Efficient ligation chemistry that increases library yield from low input helps minimize required PCR cycles.
Confirm kit compatibility with your downstream analysis pipeline
Some library prep protocols use specific adapter sequences or library structures that require corresponding adjustments in bioinformatics analysis pipelines, and confirming compatibility before sequencing helps avoid downstream analysis failures.
&nbsp;
<h2>Specifications context</h2>
&nbsp;
ChIP-seq library prep kits optimized for low-input or ultra-low-input chromatin are designed to achieve high library complexity from picogram-scale DNA inputs that would otherwise produce low-complexity libraries with standard kits at similar PCR cycle numbers. As of 2026, library prep kits compatible with enzymatic methyl-seq (EM-seq) as well as classical bisulfite-converted DNA continue to expand, enabling researchers to leverage improved DNA quality while maintaining familiar downstream sequencing workflows.
Prepared to enhance your sequencing efficiency? Discover our complete selection of NGS Library Preparation Kits and <a href="https://mbpinc.net/contact-us">contact the MBP team</a> for a quote now.

NGS Libray Preparation Kits

RRHP 5-hmC Library Prep Kit

The RRHP 5-hmC Library Prep Kit (D5450) by Zymo Research enables reduced representation hydroxymethylation profiling of 5-hmC in 12 reactions, using an enzymatic—not bisulfite—approach for genome-wide 5-hmC mapping compatible with Illumina HiSeq and MiSeq platforms. Available in 12 preps (D5450) and 25 preps (D5451).

Equipment Required

Input

Sample Source

Sequencing Compatibility

RRHP™ 5-hmC Library Prep Kit (12 Preps.)

RRHP™ 5-hmC Library Prep Kit (25 Preps.)

<h2>What are ELISA kits for methylation in this category?</h2>
&nbsp;
ELISA kits for DNA and RNA methylation in this category are antibody-based assays that quantify the global level of a specific epigenetic mark, most commonly 5-methylcytosine in genomic DNA, 5-hydroxymethylcytosine in genomic DNA, or N6-methyladenosine in RNA, using a plate-based immunoassay format without requiring bisulfite conversion or sequencing. Denatured, single-stranded DNA or RNA from a sample is coated on a plate well, and a mark-specific primary antibody followed by an HRP-conjugated secondary antibody generates a colorimetric signal proportional to the level of the target modification.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" role="presentation">5-mC DNA ELISA kits for quantitative analysis of DNA methylation&nbsp;</li>
<li dir="ltr" role="presentation">DNA controls for validation and calibration of the assay to ensure experimental&nbsp; reproducibility and accuracy&nbsp;</li>
<li dir="ltr" role="presentation">Secondary antibody reagents for specific signal generation and detection in ELISA assays</li>
<li dir="ltr" role="presentation">Coating buffers for consistent assay performance and optimized plate preparation&nbsp;</li>
</ul>
&nbsp;
<h2>How to choose methylation ELISA kits and reagents</h2>
&nbsp;
Match your kit to the specific epigenetic mark you're quantifying
Different kits use antibodies against specific modifications: 5-methylcytosine ELISA kits quantify global DNA methylation, 5-hmC ELISA kits quantify global hydroxymethylation, and m6A ELISA kits quantify RNA N6-methyladenosine. Using a kit with the wrong antibody specificity will not report the mark you intend to measure.
Use methylation standards to build a calibration curve for quantitative results
Running a series of methylation standards with defined percentages alongside your samples allows the absorbance readout to be converted to a specific, meaningful methylation percentage, since the raw ELISA signal alone cannot be interpreted as absolute methylation level without a calibration.
Understand that ELISA measures global levels, not locus-specific methylation
A methylation ELISA gives the overall average percentage of methylation across the genome in a sample, which is useful for comparing broad methylation changes between conditions but cannot identify which specific genes or regions are differentially methylated the way bisulfite sequencing can.
Confirm the required DNA denaturation step is appropriate for your sample type
ELISA kits for DNA methylation typically require single-stranded, denatured DNA coated directly on the plate, and confirming this denaturation step is properly performed is necessary for consistent antibody binding and reproducible signal across wells.
Be aware of cross-reactivity with similar modifications when interpreting results
An antibody against 5-methylcytosine may have some cross-reactivity with 5-hydroxymethylcytosine, and confirming the antibody's published cross-reactivity data helps interpret whether your signal specifically reflects 5-mC, 5-hmC, or both, which matters for studies in cell types where 5-hmC is abundant.
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<h2>Specifications context</h2>
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The 5-methylcytosine ELISA workflow uses an indirect ELISA methodology where denatured, single-stranded DNA samples are coated directly on the plate well surfaces and a 5-mC monoclonal antibody and an HRP-conjugated secondary antibody are added sequentially, generating a colorimetric signal proportional to the total level of methylated cytosine in the sample. As of 2026, methylation ELISA kits are particularly valued for high-throughput screening studies comparing global methylation levels across many treatment conditions or patient groups where single-base-resolution data is not the primary goal.
This category sits within DNA/RNA Methylation, alongside Methylation Standards for calibration, and is related to DNA Hydroxymethylation and Non-Bisulfite Kits &amp; Reagents for higher-resolution methylation analysis. See the full reagents catalog and use Quick Order for recurring orders.
<a href="https://mbpinc.net/contact-us">Contact the expert team of&nbsp; Molecular Biology Products Inc. (MBP)</a> to get high-quality ELISA Kits and Reagents for your lab.

ELISA Kits & Reagents

Secondary Antibody

Zymo Research HRP-conjugated Secondary Antibody (1 µg/µl) for 5-mC DNA ELISA Kit (D5325/D5326): detects anti-5-mC Clone 7D21 at 405 nm. Two volumes: D5325-3-15 (15 µl) and D5325-3-30 (30 µl).

Secondary Antibody (1 µg/µl) (15 µl)

Secondary Antibody (1 µg/µl) (30 µl)

<h2>What are DNA Cleanup Kits?</h2>
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DNA cleanup kits purify and concentrate pre-extracted or pre-amplified DNA by removing enzymes, salts, organic solvents (phenol, chloroform), unincorporated nucleotides, RNA, detergents, and other contaminants from DNA solutions using silica-membrane spin columns with a bind-wash-elute protocol. Unlike PCR cleanup kits that are specifically optimized to remove primers and dNTPs from PCR reactions, DNA cleanup kits accept broader input chemistries - including post-phenol-chloroform extraction DNA, genomic DNA in high-salt lysis buffers, restriction digest reactions, and dilute DNA solutions requiring concentration - and elute DNA in minimal volumes (as little as 6 ul) for immediate use in downstream applications. Use a DNA cleanup kit whenever your DNA preparation contains inhibitors incompatible with downstream enzymatic reactions, when residual phenol must be removed, or when dilute DNA must be concentrated into a small volume.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" aria-level="1">
DNA Clean &amp; Concentrator&trade; (DCC): Efficient spin-column systems (5, 25, 100, 500 preps) created to concentrate low-concentration DNA into ultra-pure, transfection-quality volumes.
</li>
<li dir="ltr" aria-level="1">
Genomic DNA Clean &amp; Concentrator: Tailored procedures for extracting large templates while maintaining genomic integrity for long-read sequencing uses.
</li>
<li dir="ltr" aria-level="1">
Select-a-Size DNA Clean &amp; Concentrator&trade;: Tailored systems for the recovery of size-specific fragments, efficiently eliminating adapter dimers and non-target amplicons.
</li>
<li dir="ltr" aria-level="1">
ZR-96 DNA Cleanup Systems: Scalable 96-well and MagBead configurations designed for high-throughput, automated processes while ensuring reproducibility-validated outcomes.
</li>
</ul>
&nbsp;
<h2>How to Choose a DNA Cleanup Kit</h2>
&nbsp;
Capacity and Input Volume
Zymo DNA Clean &amp; Concentrator kits are available in formats matched to DNA input mass: DCC-5 (&lt;=5 ug input, elute &gt;=6 ul), DCC-25 (&lt;=25 ug input, elute &gt;=25 ul), DCC-100 (&lt;=100 ug input, elute &gt;=25 ul). Choose the format whose maximum capacity exceeds your expected DNA input by at least 2-fold to avoid column overloading, which reduces yield and purity. For genomic DNA preparations from tissue (typically 5-30 ug), DCC-25 or DCC-100 is appropriate.
Minimum Elution Volume and Concentration
For maximum DNA concentration, Zymo DCC-5 elutes in 6 ul - the industry minimum for standard silica columns. If the input volume is 500 ul (1 ng/ul) and the elution is 6 ul, the final concentration reaches approximately 80 ng/ul (assuming 95% recovery), a concentration suitable for transfection, electroporation, and microinjection.
Size Selectivity
Standard DNA cleanup kits retain all DNA &gt;=100 bp. If size selection is also required, use gel extraction (for specific band isolation) or AMPure XP beads (for size-range selection by bead: volume ratio adjustment) rather than a standard cleanup kit.
Post-Phenol-Chloroform Cleanup
For DNA recovered from phenol-chloroform extraction, add 5 volumes of binding buffer and 2 volumes of 100% ethanol to the aqueous phase before column loading. The organic solvent in residual phenol or chloroform does not significantly impair column binding at these dilutions. Multiple column reloads allow processing of large aqueous-phase volumes through a single column.
RNase A Treatment for DNA-Only Preparations
For gDNA preparations that must be RNA-free for optical mapping or certain long-read sequencing library kits, add RNase A (100 ug/ml) to the DNA solution, incubate at 37 degrees C for 10 minutes, then proceed directly to DCC cleanup. The RNase digestion products are removed during the wash steps.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
Zymo DNA Clean &amp; Concentrator kits use a single-buffer system with Zymo-Spin column technology and recover DNA from PCR, enzymatic reactions, phenol-chloroform extractions, and dilute solutions. DNA is eluted in volumes as small as 6 ul, providing up to 80-fold concentration from 500 ul inputs. The kits remove enzymes, proteins, salts, organic solvents, dyes, unincorporated nucleotides, primers, and other small molecules, delivering DNA ready for restriction digestion, ligation, sequencing, Southern blotting, transfection, and long-read library preparation. DNA cleanup and concentration are standard workflow steps in genomics laboratories at Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center, where removing trace inhibitors from gDNA before library preparation significantly improves NGS library complexity and uniformity.
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Enhance your capabilities&mdash;<a href="https://mbpinc.net/contact-us">reach out to the MBP Inc. team</a> now to obtain a quote for your DNA concentration requirements.

DNA Cleanup Kits

D4080-Data Sheet

D4080-MSDS

D4080-1-MSDS

D4080-Protocol

Select-a-Size DNA Clean & Concentrator™ Kit

The Select-a-Size DNA Clean & Concentrator™ Kit is available in the following variants: D4080, D4080-1-15.The D4080 by Zymo Research is a 25-prep Select-a-Size DNA Clean &amp; Concentrator Kit that cleans up and size-selects DNA in a single spin-column workflow, with user-adjustable cutoffs at ≥50, ≥100, ≥150, ≥200, or ≥300 bp and a double-size selection mode for the 50–700 bp window. Binding capacity is up to 3 µg per prep; protocol runs in as little as 7 minutes; A260/280 &gt; 1.8 output.

Select-a-Size DNA Clean & Concentrator™ Kit (25 Preps.)

Select-A-Size Binding Buffer (15 ml)

D4084-Data Sheet

D4084/D4085-MSDS

D4084-4-MSDS

D4084-Protocol

Select-a-Size DNA Clean & Concentrator™ MagBead Kit

Zymo Research Select-a-Size DNA Clean &amp; Concentrator MagBead Kit: tunable 150–800 bp size selection in ≤10 min, up to 10 µg, ≥10 µl. Complete kit 10 mL (D4084) and 50 mL (D4085); MagBeads only 10 mL (D4084-4-10) and 50 mL (D4084-4-50).

Applicable For

Elution Volume

Equipment

Processing Time

Purity

Size Range

Yield

Select-a-Size DNA Clean & Concentrator™ MagBead Kit (10 ml)

Select-a-Size DNA Clean & Concentrator™ MagBead Kit (50 ml)

Select-a-Size MagBeads (10 ml)

Select-a-Size MagBeads (50 ml)

Plates

Silicon-A Plate (2 Plates)

Silicon-A Plate C2001 by Zymo Research is a 96-well silica-matrix plate for centrifuge-based high-throughput DNA and RNA purification, with up to 5 µg binding capacity per well, 600 µl well volume, and ≥30 µl elution. Supplied as 2 plates per pack.

DataSheet

Silicon-A™-HRC Plate (2 Plates)

C2009 by Zymo Research is the Silicon-A™-HRC Plate (2 plates, 96-well format), a replacement component for the OneStep-96 PCR Inhibitor Removal Kit (D6035). The Silicon-A™-HRC matrix removes polyphenolics, humic/fulvic acids, tannins, and melanin from DNA and RNA extracts for direct use in PCR, qPCR, or sequencing. Requires Prep Solution before use. MBP is a registered vendor for Howard Hughes Medical Institute, Vanderbilt University, MD Anderson Cancer Center, Eurofins, and many other institutes across the USA.

Columns, Plastics & Accessories

Squisher-8 w/ 96-Well Block

Zymo Research Squisher-8 w/ 96-Well Block: 8-sample-per-cycle tissue homogenizer for small solid tissues in 96-well format. Two pack sizes: H1002-20 (20 homogenizers + 2 blocks) and H1002-5 (5 homogenizers + 1 block).

Squisher-8 w/ 96-Well Block (20 Pack & 2 Blocks)

Squisher-8 w/ 96-Well Block (5 Pack & 1 Block)

Squisher-96 w/ 96-Well Block

Zymo Research Squisher-96 w/ 96-Well Block: manual 96-sample simultaneous tissue homogenizer, PP construction, guanidinium-compatible. H1004-2 (2 units + 2 blocks) and H1004-5 (5 units + 5 blocks).

Squisher-96 w/ 96-Well Block (2 Pack & 2 Blocks)

Squisher-96 w/ 96-Well Block (5 Pack & 5 Blocks)

Squisher-Single

The Squisher-Single is available in the following variants: H1001, H1001-50.H1001 by Zymo Research is the Squisher-Single, a disposable polypropylene manual pestle that homogenizes small tissue samples (liver, brain, mouse tail, insects) directly in a 1.5 mL microcentrifuge tube for downstream DNA, RNA, or protein extraction. Supplied in a pack of 10; H1001-50 provides 50 per pack. Can be cleaned and reused.

Squisher-Single (10 Pack)

Squisher-Single (50 Pack)

<h2>What are PCR Cleanup Kits?</h2>
&nbsp;
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™

Zymo Research ssDNA/RNA Clean &amp; Concentrator™: selective 17–200 nt ssDNA/ssRNA purification in ~10 min, ≥6 µl, 10 µg capacity, A260/280 &gt;1.8. D7010 (20 preps), D7011 (50 preps). Buffer components: Binding Buffer (D7010-1), Prep Buffer (D7010-2), Wash Buffer (D7010-3).