Zymo Reagents

<h2>What are RNA Cleanup Kits?</h2>
&nbsp;
RNA cleanup kits purify and concentrate pre-extracted or synthesized RNA by removing enzymes, buffer components, unincorporated NTPs, DNA contamination, organic solvents, and environmental inhibitors (humic acids, polyphenols) from RNA solutions using silica-membrane spin columns with a simple bind-wash-elute protocol in under 10 minutes. Cleanup kits are the mandatory intermediate step between primary RNA extraction or enzymatic RNA synthesis and sensitive downstream applications - including rRNA depletion, NGS library preparation, in vitro translation, and mRNA vaccine formulation - where residual enzymes or inhibitors would cause assay failure. Zymo RNA Clean &amp; Concentrator kits elute RNA in as little as 6 ul, concentrating inhibitor-free RNA from volumes up to 500 ul into a minimal volume suitable for low-input sequencing library preparation. Use an RNA cleanup kit after any enzymatic reaction that generates RNA (DNase I treatment, IVT, capping, polyadenylation) and after environmental RNA extraction when A260/A230 is below 1.5 - never skip this step and proceed directly to library preparation or rRNA depletion.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" aria-level="1">
RNA Clean &amp; Concentrator&trade; (RCC): Effective spin-column systems (5, 25, 100 preps) created to concentrate low RNA concentrations into ultra-pure volumes while eliminating dyes and inhibitors.
</li>
<li dir="ltr" aria-level="1">
ZR-96 RNA Clean &amp; Concentrator&trade;: 96-well plate formats that are scalable and tailored for high-throughput lab settings while maintaining genomic integrity.
</li>
<li dir="ltr" aria-level="1">
Magbead RNA Cleanup: Sophisticated magnetic bead technology designed for automated processes, guaranteeing reproducibility-verified outcomes and uniform recovery of total RNA.
</li>
<li dir="ltr" aria-level="1">
Small RNA Retrieval: Refined methods that enhance the preservation of microRNA and various small RNA types, crucial for precise isoform identification and bioinformatics evaluation.
</li>
</ul>
&nbsp;
<h2>How to Choose an RNA Cleanup Kit</h2>
&nbsp;
Binding Capacity (Format Selection)
Match the kit format to your expected RNA input mass to avoid overloading: Zymo RCC-5 (&lt;=10 ug, elute &gt;=6 ul) for routine RT-qPCR and small-batch RNA-seq cleanup; RCC-25 (&lt;=50 ug, elute &gt;=25 ul) for standard IVT and RNA-seq preparations; RCC-100 (&lt;=100 ug, elute &gt;=30 ul) for large-scale IVT or mRNA synthesis; NEB Monarch 500 ug format for high-yield preparative IVT in mRNA vaccine development. Overloading reduces yield nonlinearly; test a small input aliquot first if the expected yield is uncertain.
DNase I-Included vs. DNase-Free Formats
Zymo RCC kits catalog numbers R1013 and R1014 include DNase I for gDNA removal during cleanup - combining the DNase treatment and concentration into a single column workflow. For RNA samples where gDNA contamination is confirmed (co-extracted total RNA, environmental RNA), use the DNase I-included format. For IVT RNA (no genomic DNA present) or post-DNase RNA that only needs cleanup, use the standard RCC format without DNase.
Size-Selective Recovery
Adjust ethanol ratio in the binding step for size-selective cleanup: total RNA (&gt;=17 nt) uses a high ethanol ratio; large RNA-only (&gt;200 nt) uses a lower ratio; small RNA (17-200 nt) is collected from the flow-through of the large RNA step and rebound on a second column at high ethanol. This two-step selection from one sample enables preparation of paired large RNA and small RNA fractions for simultaneous mRNA-seq and miRNA-seq library preparation without separate primary extraction.
Environmental RNA Inhibitor Removal
For soil or fecal RNA with A260/A230 below 1.5, RCC-5 cleanup consistently raises A260/A230 to &gt;1.8 by binding RNA and washing away humic acids, polyphenolics, and fulvic acids. Run the cleanup before proceeding to rRNA depletion - inhibitor-contaminated RNA causes inefficient depletion, wasting expensive reagents. Add an RNA quantification step (Qubit RNA HS Assay) before and after cleanup to confirm both recovery and inhibitor removal.
mRNA vs. Total RNA
For mRNA-specific applications (mRNA vaccine, mRNA for in vitro translation), cleanup removes abortive transcripts, DNA template, and IVT enzymes from the desired full-length mRNA. For total RNA from cells or tissue (containing rRNA, mRNA, tRNA, and small RNA), the cleanup removes extraction reagent contamination before rRNA depletion or library preparation.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
Zymo RNA Clean &amp; Concentrator kits use a single-buffer system with Zymo-Spin IC column technology, recovering total RNA &gt;=17 nt, large RNA &gt;200 nt, or small RNA 17-200 nt by adjusting ethanol conditions. RNA is eluted in as little as 6 ul of RNase-free water, ready for RT-qPCR, RNA-seq, hybridization, and sequencing without further processing. The kits remove enzymes, NTPs, unincorporated nucleotides, humic acid, polyphenolics, dyes, salts, and organic solvents from RNA solutions. RNA cleanup is a standard workflow step in metatranscriptomics (before rRNA depletion from environmental RNA), mRNA vaccine development (IVT product cleanup before formulation), and RNA-seq library preparation (cleanup after DNase I treatment) at institutions including Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center.
&nbsp;
Ensure your RNA quality and eliminate interference&mdash;<a href="https://mbpinc.net/contact-us">get in touch with MBP Inc.</a> now to obtain a quote for your RNA purification reagents.

RNA Cleanup Kits

Protocol

DataSheet

MSDS

RNA Clean & Concentrator™-100 (25 Preps.)

R1019 by Zymo Research is the RNA Clean &amp; Concentrator™-100 (25 preps), a large-format spin-column kit with 1 mg RNA binding capacity that recovers &gt;90% of total RNA ≥17 nt in 5 minutes, eluting in 100 µL with A260/A280 and A260/A230 &gt;1.8 — for NGS, RT-qPCR, and high-yield RNA preparations.

Equipment

Format

Purity

Sample Source

Size Range

Yield

Manufacturer

Shipping Condition

Storage Condition

RNA Clean & Concentrator™-25

R1017 by Zymo Research is the RNA Clean &amp; Concentrator™-25 (50 preps), a 5-minute spin-column kit that recovers &gt;90% of total RNA ≥17 nt from enzymatic reactions, DNase-treated samples, IVT products, and TRIzol extracts, with elution in as little as 25 µL for NGS, RT-qPCR, and microarray applications.

RNA Clean & Concentrator™-25 (50 Preps.)

RNA Clean & Concentrator™-25 (100 Preps.)

MSDS - R1013/R1014

R1013-MSDS - R1015/R1016

RNA Clean & Concentrator™-5

RNA Clean &amp; Concentrator-5 (R1013) by Zymo Research — 5-minute RNA cleanup and concentration with &ge;90% recovery, elution in as little as 6 µL, and on-column DNase I digestion included. Handles &ge;17 nt RNA; 50 preps per kit.

RNA Clean & Concentrator™-5 (50 Preps.)(DNase Included)

RNA Clean & Concentrator™-5 (200 Preps.)(DNase Included)

RNA Clean & Concentrator™-5 (50 Preps.)(DNase not Included)

RNA Clean & Concentrator™-5 (200 Preps.)(DNase not Included)

RNA Binding Buffer (100 ml)

RNA Binding Buffer (25 ml)

RNA Binding Buffer (50 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

RNA Conversion Reagent (1.5 ml)

RNA Conversion Reagent R5001-1-1 by Zymo Research is a 1.5 ml ready-to-use bisulfite conversion reagent sold as a standalone replacement component for the EZ RNA Methylation Kit (R5001, R5002). It converts unmethylated cytosines to uracil while preserving 5-methylcytosine for RNA methylation analysis. Stored at room temperature.

RNA Desulphonation Buffer

RNA Desulphonation Buffer by Zymo Research is available in 10 ml (R5001-3-10) and 40 ml (R5001-3-40) formats for in-column desulphonation of bisulfite-converted RNA, stored at room temperature. Compatible with the EZ RNA Methylation Kit (R5001, R5002) for epitranscriptomic RNA methylation analysis; sold as a standalone replenishment reagent. MBP is a registered vendor for Howard Hughes Medical Institute, Vanderbilt University, MD Anderson Cancer Center, and many more leading research institutes, serving labs across the United States, Canada, and internationally.

RNA Desulphonation Buffer (10 ml)

RNA Desulphonation Buffer (40 ml)

<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
&nbsp;

Zymo Buffers

RNA Lysis Buffer

RNA Lysis Buffer R1060-1-100 by Zymo Research — 100 ml lysis and RNase-inactivation buffer for Quick-RNA kit workflows. Use 300–600 µL per ≤10⁷ cells or 1:1 with processed tissue/blood supernatants. Room-temperature storage; also available in 50 ml (R1060-1-50). Order via <a href="https://www.mbpinc.net/quickorder">Quick Order</a> or contact <a href="mailto:customerservice@mbpinc.net">customerservice@mbpinc.net</a>.

RNA Lysis Buffer (100 ml)

RNA Lysis Buffer (50 ml)

RNA MAX Buffer (20 ml)

RNA MAX Buffer (R1070-2-20) by Zymo Research — 20 ml RNA-binding buffer for the ZR small-RNA PAGE Recovery Kit. Recovers ≥50% of 17–28 nt small RNA from flow-through fractions. A260/A280 &gt;1.8. Room temperature storage.

RNA MagBead Binding Buffer (15 ml)

R1081-1-15 by Zymo Research is a 15 ml RNA binding buffer component for use with Zymo Research magnetic bead-based RNA purification kits, sold as a standalone SKU. Lab managers running high-throughput RNA isolation can reorder the binding buffer independently when it is consumed before other kit reagents, keeping automated workflows running without full kit repurchase.

RNA Pre-Wash Buffer

RNA Pre-Wash Buffer by Zymo Research: wash buffer for the Quick-RNA Midiprep Kit total RNA purification workflow. Intermediate wash step that removes contaminants from the silica membrane before RNA elution. Available in multiple sizes. Research use only.

RNA Pre-Wash Buffer (100 ml)

RNA Pre-Wash Buffer (12 ml)

RNA Pre-Wash Buffer (25 ml)

RNA Pre-Wash Buffer (50 ml)

RNA Prep Buffer

RNA Prep Buffer R1060-2-10 by Zymo Research — 10 ml column washing buffer for Zymo RNA purification kits including the Quick-RNA Microprep Kit (R1050). Sold separately for independent buffer replenishment; also available in 25, 50, and 100 ml sizes. Order via <a href="https://www.mbpinc.net/quickorder">Quick Order</a> or contact <a href="mailto:customerservice@mbpinc.net">customerservice@mbpinc.net</a>.

RNA Prep Buffer (10 ml)

RNA Prep Buffer (100 ml)

RNA Prep Buffer (25 ml)

RNA Prep Buffer (50 ml)

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.

<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.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
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.
&nbsp;
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

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.