Nucleic Acid Cleanup Kits

<h2>What are DNA Cleanup Kits?</h2>
&nbsp;
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.
&nbsp;
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

MSDS

Brochure

Protocol

DNA Clean & Concentrator Magbead Kit (100 preps)

D4012 by Zymo Research is a 100-prep magnetic bead DNA cleanup kit compatible with any open liquid handler or magnetic bead mover. Recovers DNA ≥25 bp (up to 150 kb HMW); &gt;90% recovery for ≥100 bp fragments; purity A260/A280 &amp; A260/A230 ≥1.8; elution in 30–50 µl. Suitable for PCR cleanup, NGS library prep, restriction digests, and automated high-throughput purification.

Binding Capacity

Purity

Sample Sources

Size

Manufacturer

Shipping Condition

Storage Condition

DNA Clean & Concentrator-100

D4029 by Zymo Research is the DNA Clean &amp; Concentrator-100 kit for purifying up to 100 µg of DNA from PCR, large restriction digests, or cell-free lysates — 25 preps, &lt;20 min, ≥150 µL elution, 70–95% recovery for 50 bp–10 kb.

Detergent Tolerance

Elution Volume

Equipment

Sample Source

Size Range

Yield

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

DNA Clean & Concentrator™-100 (50 Preps.)

DataSheet

DNA Clean & Concentrator-25

D4005 by Zymo Research is the DNA Clean &amp; Concentrator-25, recovering up to 25 µg of DNA from PCR products, restriction digests, and enzymatic reactions in ~2 minutes with 70–90% recovery for fragments 50 bp–10 kb. Samples are eluted in ≥25 µl of water or Tris buffer and are ready for sequencing, ligation, and NGS library preparation.

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

DNA Clean & Concentrator™-25 (200 Preps.)

D4033 by Zymo Research — DNA Clean &amp; Concentrator-25, 50 preps. Purifies DNA from PCR and enzymatic reactions in ~2 minutes with up to 25 µg binding capacity and elution in as little as 25 µl. Recovery: 70–90% for 50 bp–10 kb fragments.

DNA Clean & Concentrator-500

DNA Clean &amp; Concentrator-500 D4031 by Zymo Research purifies and concentrates up to 500 µg of DNA from large-scale restriction digests, crude preparations, and high-mass PCR reactions in under 20 minutes, with 70–95% recovery for 50 bp–10 kb fragments. 10 preps per kit.

DNA Clean & Concentrator™-500 (10 Preps.)

DNA Clean & Concentrator™-500 (20 Preps.)

DNA Clean & Concentrator™-5

D4003 by Zymo Research — DNA Clean & Concentrator-5; 50 preps; 2-minute cleanup; ≥6 µL elution; 50 bp–23 kb; ≤5 µg binding capacity; A260/A280 > 1.8; removes enzymes, dNTPs, and buffers from PCR and enzymatic reactions.

DNA Clean & Concentrator™-5 (50 Preps.) (Uncapped)

DNA Clean & Concentrator™-5 Kit (10 Preps.)(Uncapped)

DNA Clean & Concentrator™-5 (200 Preps.)(Uncapped)

DNA Clean & Concentrator™-5 (50 Preps.) (Capped)

DNA Clean & Concentrator™-5 (200 Preps.) (Capped)

DNA Binding Buffer (25 ml)

DNA Binding Buffer (50 ml)

DNA Wash Buffer (Concentrate) (24 ml)

DNA Wash Buffer (Concentrate) (48 ml)

DNA Wash Buffer (Concentrate) (6 ml)

DNA Binding Buffer (100 ml)

D4064-MSDS

D4064-Protocol

Genomic DNA Clean & Concentrator™ Kit-25

D4064 by Zymo Research — Genomic DNA Clean &amp; Concentrator™-25 Kit (25 preps). Purifies and concentrates up to 25 µg high molecular weight DNA (50 bp to 200 kb) from enzymatic reactions and dilute samples in ~5 minutes. Elution ≥ 35 µl; recovery 70–95%; A260/A280 &gt; 1.8. Also available as D4065 (100 preps).

Applicable For

Sample storage

Genomic DNA Clean & Concentrator™ Kit-25 (25 Preps.)

Genomic DNA Clean & Concentrator™ Kit-25 (100 Preps.)

Genomic DNA Clean & Concentrator™-10 Kit

D4010 by Zymo Research is the Genomic DNA Clean &amp; Concentrator™-10, purifying and concentrating gDNA, BAC/PAC DNA, viral DNA, and WGA products up to 200 kb in ~5 minutes with 70–95% recovery. Binding capacity is 10 µg; elution volume ≥10 µl; purity A260/A280 &gt;1.8 and A260/A230 &gt;1.8.

Sample Storage

Genomic DNA Clean & Concentrator™-10 Kit (25 Preps.)

Genomic DNA Clean & Concentrator™-10 Kit (100 Preps.)

<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.
&nbsp;
<h2 dir="ltr">What you will find:</h2>
&nbsp;
<ul>
<li dir="ltr" aria-level="1">
Oligo Clean &amp; Concentrator: Precisely designed systems for the quick retrieval of single-stranded DNA, RNA, and oligonucleotides from enzymatic processes.
</li>
<li dir="ltr" aria-level="1">
OneStep&trade; PCR Inhibitor Removal: Tailored columns and 96-well formats engineered to eliminate polyphenols, humic acids, and lipids that hinder PCR kinetics.
</li>
<li dir="ltr" aria-level="1">
ssDNA/RNA Clean &amp; Concentrator&trade;: An adaptable method for purifying and concentrating small nucleic acid segments, ensuring isoform specificity.
</li>
<li dir="ltr" aria-level="1">
ZR-96 High-Throughput Systems: Scalable formats of 96-well plates designed for automated lab processes, guaranteeing reproducibility-validated outcomes across extensive sample groups.
</li>
</ul>
&nbsp;
<h2>How to Choose a PCR Cleanup Kit</h2>
&nbsp;
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.
&nbsp;
<h2>Specifications Context</h2>
&nbsp;
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.
&nbsp;
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

D4060-1-Data Sheet

D4060 - MSDS

D4061 - MSDS

D4060-1 - MSDS

D4060-1-Protocol

Oligo Clean & Concentrator

D4060-1 by Zymo Research is the Oligo Clean &amp; Concentrator — a spin-column kit that purifies DNA and RNA oligonucleotides (≥16 nt) in approximately 2 minutes with &gt;90% recovery, eluting in as little as 6 µL for use in hybridization, sequencing, and PCR applications.

Oligo Clean & Concentrator (50 Preps.)

Oligo Clean & Concentrator (200 Preps.)

Oligo Binding Buffer (10 ml)

Oligo Binding Buffer (40 ml)

MSDS - D6035

MSDS - D6035-1-30

Protocol - D6035

OneStep-96™ PCR Inhibitor Removal Kit

OneStep-96™ PCR Inhibitor Removal Kit (D6035) by Zymo Research — 96-well format, 192 preps total. Removes humic/fulvic acids, polyphenols, tannins, and melanin from DNA and RNA extracts in a single step with no centrifugation.

Type

OneStep-96™ PCR Inhibitor Removal Kit (2 x 96 Preps.)

Prep Solution (30 ml)

MSDS - D6030

MSDS - D6031

Protocol - D6030

Protocol - D6031

OneStep™ PCR Inhibitor Removal Kit

D6030 OneStep PCR Inhibitor Removal Kit by Zymo Research — 50 preps, removes humic acids, tannins, melanin in ~1 min, 50–200 µl input and elution, room-temperature storage.

OneStep™ PCR Inhibitor Removal Kit (50 Preps.)

OneStep™ PCR Inhibitor Removal Kit (Updated) (50 Preps.)

<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

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.

Format

United States

Texas

mbpinc