Nucleic Acid Cleanup Kits

<h2>What are RNA Cleanup Kits?</h2>
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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.
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<h2 dir="ltr">What you will find:</h2>
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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.
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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.
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Magbead RNA Cleanup: Sophisticated magnetic bead technology designed for automated processes, guaranteeing reproducibility-verified outcomes and uniform recovery of total RNA.
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Small RNA Retrieval: Refined methods that enhance the preservation of microRNA and various small RNA types, crucial for precise isoform identification and bioinformatics evaluation.
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<h2>How to Choose an RNA Cleanup Kit</h2>
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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.
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<h2>Specifications Context</h2>
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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.
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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

MSDS

DataSheet

Protocol

ZR-96 RNA Clean & Concentrator™ Magbead Kit (96 Preps.)

ZR-96 RNA Clean & Concentrator™ MagBead Kit (R1081) by Zymo Research purifies and concentrates total RNA (≥17 nt, up to 10 µg per prep) in 96-well format using magnetic beads, with a minimum 15 µl elution volume. Compatible with automated liquid handlers and bead movers for high-throughput RNA cleanup from DNase I-treated RNA, TRIzol aqueous phases, and in vitro transcription products.

Binding Capacity

Equipment

Purity

RNA Storage

Sample Sources

Size Range

Manufacturer

Shipping Condition

Storage Condition

ZR-96 RNA Clean & Concentrator™ Magbead Kit (with DNase I) (96 Preps.)

<h2>What are Gel Extraction Kits?</h2>
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Gel extraction kits (gel purification or gel DNA recovery kits) isolate specific DNA fragments from standard and low-melting agarose gels after electrophoresis by dissolving the excised gel band in a chaotropic buffer that melts agarose and conditions DNA to bind a Zymo-Spin followed by washing to remove agarose, gel stains (EtBr, SYBR Safe, GelRed), salts, and proteins, and elution in 30-50 ul. Gel extraction is the primary method for isolating specific DNA fragments from multi-band reactions - PCR amplifications producing non-specific products, restriction digests generating multiple fragments, and vector preparations requiring removal of small insert-incompatible fragments. Use gel extraction instead of direct PCR cleanup whenever the reaction produces more than one visible band and only a specific size is needed downstream; for single-band reactions, PCR cleanup recovers 10-20% more DNA in the same protocol time.
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Zymoclean&trade; Gel DNA &amp; RNA Recovery: Innovative spin-column systems created for quick extraction of nucleic acids without any salt or agarose contamination.
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ZR small-RNA&trade; PAGE Recovery: A dedicated method for the accurate isolation of microRNA and small RNA types from polyacrylamide gels, preserving isoform uniqueness.
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Large Fragment DNA Recovery: Designed methods for the careful elution of high-molecular-weight DNA, avoiding mechanical shearing for extended-read sequencing.
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High-Throughput &amp; Universal Kits: Adaptable ZR-96 formats and flexible Column-Pure systems designed for standard laboratory cleanup and automated processes.
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<h2>How to Choose a Gel Extraction Kit</h2>
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Fragment Size Range
Standard silica-column gel extraction kits ( Zymo Zymoclean, Thermo Fisher GeneJET) purify 70 bp to 10 kb with &gt;80% recovery for 200 bp-5 kb.&nbsp; For fragments larger than 10 kb requiring size-selective gel purification, use electroelution, agarase digestion of low-melting agarose, or pulse-field gel extraction followed by alcohol precipitation.
Agarose Percentage and Dissolution Protocol
For standard 0.8-2% agarose gels: use 3 volumes of dissolution buffer per 1 volume (weight:volume) of gel slice at 50-60 degrees C for 5-10 minutes. For high-percentage gels (&gt;2%): use 6 volumes of dissolution buffer and extend incubation to 10-15 minutes, or add isopropanol to help dissolve the denser agarose matrix. Incomplete dissolution is the most common cause of low yield and must be verified visually - no visible agarose particles should remain in the dissolved solution before loading the column.
Elution Volume
For cloning applications where insert concentration matters, use the minimum elution volume (30-35 ul) to maximize insert concentration for ligation. For sequencing of gel-purified products, elute in 30-50 ul and measure concentration by Qubit or NanoDrop before use.&nbsp;
UV Exposure Minimization
UV transilluminator exposure damages DNA via pyrimidine dimer formation, reducing downstream PCR amplification and sequencing efficiency. Limit UV exposure to &lt;30 seconds when excising bands; use a long-wavelength (365 nm) UV source instead of short-wavelength (254 nm) to minimize damage. Alternatively, use a blue-light transilluminator (Safe-Imager, Clare Chemical DarkReader) with SYBR Safe or GelRed stain, which causes no photodamage to DNA during band excision.
Column vs. Magnetic Bead Gel Extraction
Standard gel extraction uses spin columns. For 96-well high-throughput gel extraction applications, vacuum-manifold compatible 96-well plate formats (Norgen DNA Gel Extraction Kit 96-well) process multiple samples simultaneously. AMPure XP magnetic beads can perform gel-alternative size selection from solution without the gel step, which avoids UV damage entirely and is preferred in NGS library preparation workflows where fragment size distribution rather than specific band isolation is the goal.
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<h2>Specifications Context</h2>
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Key benchmarks for gel extraction kits: &gt;=70% recovery for 200 bp-5 kb fragments from 1% TAE agarose gels, A260/A280 &gt;= 1.7 in eluate, no detectable agarose (confirmed by no viscosity increase in eluate), and complete removal of gel stain and EtBr (confirmed by absence of stain fluorescence in eluate). The Zymo Zymoclean Gel DNA Recovery Kit purifies DNA from TAE or TBE gels using Zymo-Spin technology, eluting in as little as 6 ul for highly concentrated DNA in minutes. Gel extraction remains an essential cloning technique at academic molecular biology labs, with blue-light transilluminator-based band excision increasingly replacing UV-based methods to protect DNA integrity during size selection.
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Unleash the genetic capabilities of your samples&mdash;<a href="https://mbpinc.net/contact-us">reach out to MBP Inc.</a> now to obtain a quote for our gel recovery services.

Gel Extraction Kits

ZR-96 Zymoclean™ Gel DNA Recovery Kit

D4021 by Zymo Research is the ZR-96 Zymoclean™ Gel DNA Recovery Kit for high-throughput gel DNA purification in a 96-well plate format — 2 x 96 preps per kit. Recovers 50 bp to 23 kbp at 70–90% efficiency with ≥15 µL elution volume and A260/A280 &gt;1.8 purity. Requires centrifuge with microplate carriers (60 mm).

Applicable For

Elution Volume

Sample Source

Yield

ZR-96 Zymoclean™ Gel DNA Recovery Kit (2 x 96 Preps.)

ZR-96 Zymoclean™ Gel DNA Recovery Kit (4 x 96 Preps.)

Zymoclean™ Gel DNA Recovery Kit (Capped)

D4007 by Zymo Research purifies DNA from TAE/TBE agarose gel slices (50 bp–23 kb) using a capped Zymo-Spin column in a 50-prep kit. Recovers up to 5 µg per column with elution in ≥6 µL and A260/A280 &gt;1.8 purity. Capped format supports easy sample labeling.

Zymoclean™ Gel DNA Recovery Kit (50 Preps.)

Zymoclean™ Gel DNA Recovery Kit (200 Preps.)

Zymoclean™ Gel DNA Recovery Kit (Uncapped)

D4001-1 by Zymo Research is the Zymoclean™ Gel DNA Recovery Kit (Uncapped) in 50-prep format, recovering DNA (50 bp–23 kb) from agarose gel slices with 70–90% efficiency (50 bp–10 kb) and eluting into ≥6 µl at A260/A280 &gt;1.8. Zymo-Spin I uncapped columns enable vacuum manifold processing and standard microcentrifuge use.

ADB (Agarose Dissolving Buffer) (100 ml)

ADB (Agarose Dissolving Buffer) (50 ml)

Zymoclean™ Gel DNA Recovery Kit (Uncapped) D4001T by Zymo Research recovers DNA from TAE/TBE agarose gels with 70–90% efficiency for fragments 50 bp–10 kb, eluting into ≥6 µl of high-concentration, NGS-ready DNA. Includes uncapped Zymo-Spin™ I columns for vacuum manifold compatibility. 10 preps per kit.

Zymoclean™ Gel DNA Recovery Kit (10 Preps.)

R1011-1-50 - MSDS

Zymoclean™ Gel RNA Recovery Kit (50 Preps.)

Zymoclean Gel RNA Recovery Kit R1011 by Zymo Research: ≥80% recovery of RNA >500 nt from agarose gel slices in ~30 minutes. Accepts TAE, TBE, and MOPS gels including formaldehyde gels up to 2.0%. Elution in ≥6 µl; binding capacity 10 µg per column. 50 preps. DNase/RNase-free.

Zymoclean™ Large Fragment DNA Recovery Kit

D4045 by Zymo Research is the Zymoclean™ Large Fragment DNA Recovery Kit (25 preps) for high-efficiency purification of DNA fragments from ~50 bp to &gt;200 kb from agarose gels, with 70–95% recovery in approximately 15 minutes using Zymo-Spin IC-XL columns and no organic solvents.

Sample storage

Type

Zymoclean™ Large Fragment DNA Recovery Kit (25 Preps.)

Zymoclean™ Large Fragment DNA Recovery Kit (100 Preps.)

<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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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.