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DNA Clean & Concentrator™-5

Clean and concentrate up to 5 μg DNA with ≥ 6 μl elution in as little as 2 minutes with 0 μl wash residue carryover.
Column design allows DNA to be eluted at high concentrations into minimal volumes of water or TE buffer.
Eluted DNA is well suited for use in PCR, DNA sequencing, DNA ligation, endonuclease digestion, RNA transcription, radiolabeling, arrays, etc.

Product Size Catalog # Price Qty
DNA Clean & Concentrator™-5 10 Preps D4003T
DNA Clean & Concentrator™-5 - Uncapped Columns 50 Preps D4003
DNA Clean & Concentrator™-5 - Uncapped Columns 200 Preps D4004
DNA Clean & Concentrator™-5 - Capped Columns 50 Preps D4013
DNA Clean & Concentrator™-5 - Capped Columns 200 Preps D4014

About DNA Clean & Concentrator™-5

The DNA Clean & Concentrator™-5 product provides purification of up to 5 µg DNA from PCR, endonuclease digestions, DNA modification reactions, isotope/fluorescence labeling reactions, etc. This product facilitate the removal of DNA polymerases, modifying enzymes, RNA polymerases, ligases, kinases, nucleases, phosphatases, and restriction endonucleases, as well as free dNTPs and their analogs including radiolabeled and fluorescent derivatives. Eluted DNA is suitable for PCR, arrays, ligation, sequencing, etc.

Format Spin Column (capped/uncapped)
DNA Recovery Typically, ≤5 µg total DNA can be eluted with ≥6 µl water or low salt elution buffer. For DNA 50 bp to 10 kb the recovery is 70-95%. For DNA 11 kb to 23 kb the recovery is 50-70%.
Equipment Microcentrifuge
DNA Size Limits 50 bp to 23 kb
Sample Sources DNA from PCR, endonuclease digestions, DNA modification reactions, isotope/fluorescence labeling reactions, etc.
DNA Purity Highly purified DNA is eluted with water and is especially well suited for sequencing, ligation reactions, and restriction endonuclease digestions.
Product Detergent Tolerance ≤5% Triton X-100, ≤5% Tween-20, ≤5% Sarkosyl, ≤0.1% SDS

Clean & Concentrated DNA. DNA samples, such as the PCR products shown here, can be efficiently purified and concentrated using the DNA Clean & Concentrator™-5

Step 1

In a 1.5 ml microcentrifuge tube, add 2-7 volumes of DNA Binding Buffer to each volume of DNA sample (see table below).  Mix briefly by vortexing.


DNA Binding Buffer  :  Sample


Plasmid, genomic DNA (>2 kb)

2  :  1

200 µl  :  100 µl

PCR product, DNA fragment

5  :  1

500 µl  :  100 µl

ssDNA1 (e.g. cDNA, M13 phage)

7  :  1

700 µl  :  100 µl

For efficient recovery of genomic or large DNA (< 20 kb to < 200 kb), use the Genomic DNA Clean & Concentrator™ (Cat. Nos. D4010, D4011).

Step 2

Transfer mixture to a provided Zymo-Spin™ Column2 in a Collection Tube.

Step 3

Centrifuge for 30 seconds.  Discard the flow-through.

Step 4

Add 200 µl DNA Wash Buffer to the column.  Centrifuge for 30 seconds.  Repeat the wash step.

Step 5

Add ≥ 6 µl DNA Elution Buffer3 or water4 directly to the column matrix and incubate at room temperature for one minute.  Transfer the column to a 1.5 ml microcentrifuge tube and centrifuge for 30 seconds to elute the DNA.

Ultra-pure DNA is now ready for use.

For specific notes and additional information, please see the product protocol PDF.

Product FAQs

  • Lower size limit of ssDNA, I have a 60nt oligo?

    The lower limit cutoff for the DNA Clean and Concentrator -5 is 50 bp of dsDNA.  Your 60 nt single stranded oligo will not bind as strongly as a 60 bp ds DNA fragment and should effectively be removed from your sample during purification.  That said, trace amounts of this oligo may still be present due to any inherent secondary structure or partial/complete annealing to your cDNA sample.  To more completely remove this 60 nt oligo, try heating your sample to 50 C for a few minutes immediately prior to adding DNA Binding Buffer.  Then, continue on with the protocol as usual.

  • Can you show it can clean up 50 bp fragments?

  • Can I use lower volumes of DBB for recovery of ss cDNA?

    Two volume of Binding Buffer works fine in most situation.  However, due to different buffer recipes and pH, especially after NaOH degradation of RNA in cDNA synthesis, we recommend to use up to 7 volumes of binding buffer for consistent yield and performance. There is no change in buffer and other components for this kit.

  • I accidentally added 2 vol. of EtOH instead of DBB to my samples (100 ul sample + 200 ul EtOH). What should I do?

    Add 2 vol additionally of DBB to the mixture.

  • My samples are floating out of my gels, why and how can I prevent it?

    Incomplete centrifugation of the columns after adding the wash buffer will cause this problem. Increase the centrifuge time (up to 1 minute or more) at maximum speed to ensure complete removal of the ethanol from the column.

  • I'm getting low recovery

    Improperly Prepared/Stored DNA Wash Buffer  

    Make sure ethanol has been added to the DNA Wash Buffer concentrate.  Cap the bottle tightly to prevent evaporation over time.

    Addition of DNA Elution Buffer

    Add elution buffer directly to the column matrix and not to the walls of the column.  Elution buffer requires contact with the matrix for at least 1 minute for large DNA ≥ 10 kb.

    Incomplete Elution

    DNA elution is dependent on pH, temperature, and time.  For large genomic DNA (≥ 50 kb), apply heated elution buffer (60-70 °C) and incubate for several minutes prior to elution.

    Sequential elutions may be performed for quantitatively higher recovery but lower final DNA concentration.  This is recommended for DNA ≥ 10 kb.

  • My A260/A230 Ratios are low

    Column Tip Contaminated

    When removing the column from the collection tube, be careful that the tip of the column does not come into contact with the flowthrough.  Trace amounts of salt from the flowthrough can contaminate a sample resulting in low A260/A230 ratios.  Ethanol contamination from the flowthrough can also interfere with DNA elution.  Zymo-Spin™ columns are designed for complete elution with no buffer retention or carryover.

  • Following Clean-up with the DCC™, Multiple Bands Appear in an Agarose Gel

    Acidification of DNA Loading Dye

    Most loading dyes do not contain EDTA and will acidify (pH ≤ 4) over time due to some microbial growth. This low pH is enough to cause DNA degradation.  Therefore, if water is used to elute the DNA, 6X Loading Dye containing 1 mM EDTA is recommended.

  • I am experiencing poor recoveries, do you have any tips?

    1)  Ensure that your entire sample flows through the column after each centrifugation.

    2)  Remember to empty the collection tube when advised.

    3)  Be careful that the tip of the column does not come into contact with the flowthrough when removing the column from the collection tube.

    4)  Extend the final wash spin by 1-2 minutes to ensure complete wash buffer removal.

    5)  Add your elution buffer directly to the column matrix, not to the walls of the column.

  • How do you compare with supplier Q?
      DCC™-5 Supplier Q
    Protocol Simple Complicated
    Processing Time 2 min. > 5 min.
    Column Binding Capacity 5 µg 5 µg
    Minimal Elution Volume 6 µl 10 µl
    Maximum DNA Concentration 0.8 µg/µl 0.5 µg/µl
    Wash Residue Carryover No Yes
    Kit Storage Room Temp. Columns @ 4°C
    Average Cost per Prep. $1.23 $2.07
    96-well Format Yes No
Submit your Citation
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Featured Citations

PCR products were purified using the DNA Clean & Concentrator™-5 for CRISPR sgRNA oligo synthesis and then used as template for in vitro transcription. This reverse genetic screening strategy, which incorporated Cas9-encoding mRNA in zebrafish, was used to examine 48 loci, resulting in the identification of two new genes involved in electrical-synapse formation by deep sequencing.
Genomic DNA from P. obducens, the causal agent of downy mildew disease, was crudely extracted and then purified using the DNA Clean & Concentrator™-5. Simple sequence repeat (SSR) markers were developed, which can be used to further assess variation in pathogen population and factors of disease emergence.
DNA from anaerobic microbial strains was extracted from meteorites and the PCR products were purified using the DNA Clean & Concentrator™-5. Phylogenetic analysis by 16S rRNA sequencing showed common bacterial genera including Bacillus and Clostridium, which may indicate contamination from modern microbes in soil.
Drosophila RNA was first NRO-modified and then reverse transcribed to generate global run-on sequencing (GRO-seq) libraries. This was further concentrated using the DNA Clean & Concentrator™-5. This detailed protocol described allows for the complete analysis of genome wide transcription in gene expression, providing information about the position, orientation, and amount of RNA transcription related polymerases.
sgRNA and repair template vectors incorporated in a CRISPR/Cas 9 system was further cleaned up using the DNA Clean & Concentrator™-5 Kit. This improved CRISPR genome editing construct combined an antibiotic resistance gene to select for repair mechanisms and also contained a fluorescent visual marker for identification of recombinant animals.
Zebrafish genomic DNA was first purified by DNAzol® and repurified using the DNA Clean & Concentrator-5™ in a study of dynamic DNA methylation expression levels during different development stages. Results showed that timing of variations in methylation patterns were specific for genes related to growth.
The DNA Clean & Concentrator-5™ was used to concentrate Pfunkel mutagenic libraries to transform into electrocompetent cells for later plasmid purification. This contributed to a novel gene tiling procedure for the function mapping of entire protein sequences.
The DNA Clean & Concentrator™-5 from Zymo Research was used to purify PCR products during cloning steps in a study that tested the strength and compatibility of varying transcription terminators, which often need to be used in series to stop transcription originating from the strong promoters required in synthetic circuits. Data from this study highlighted 39 terminators that not only have the ability to reduce downstream expression by >50-fold, but also have enough sequence diversity to be used together.
The DNA Clean & Concentrator™-5 was used to purify the enriched methylated DNA fractions as part of a methylated DNA immunoprecipitation (MeDIP) sequencing protocol. This allowed comparisons between bisulfite sequencing, MeDIP sequencing and methyl DNA Binding sequencing in the resolution of a whole genome methylation profile.

"I had low-volume, low-concentration, high-molecular weight genomic DNAs for high-throughput sequencing that I could not get to be perfectly clean without losing a significant amount of my (precious) sample. The Qiagen products were recommended by the company doing the sequencing, and they just ate up my sample. When I received this sample with my mini-prep kit, I was at the end of the line and figured I'd give it a try, despite being warned against anything involving spin columns that may shear the DNA. It worked beautifully. We can proceed with our project. No loss of sample, the gel looks the same (no sign of DNA shearing), and what an easy and fast protocol! Thank you, Zymo!"
Cindy T. (University of Iowa)
“I sampled this kit next to a kit we already use. I had three of the same sample, two for the Zymo kit and one for the other. On one of the ones designated for your kit, I accidentally added the sample directly to the column filter, then added other reagents (I figured I might as well try it). The other I did as per the instructions. The one on which I goofed gave a similar purification and concentration as the other kit, while the one I did properly yielded approximately four times the DNA per µL as the other kit. I am very happy with this result, and when I rerun my samples, I plan to use your product.”
Rosalind P. (University of Arkansas for Medical Sciences)
“I like the enhanced design of the column as it funnels every drop of volume directly through the silica in a very efficient manner. The quick spin times and relative ease of use are also a big draw as it cuts down on processing time and allows the attack of subsequent enzymatic steps at a heightened pace.”
Joseph R. (Miller School of Medicine, University of Miami)
“Almost no loss of elution buffer at the final step. It is quite impressive compared to the other kits I have used, which lose about 5-7µl.”
Takashi K. (Monash University)
“It was a very simple procedure and it gave a concentration ten times the original amount.”
Kimberly M. (University of Pennsylvania)
“It only took 2 minutes for the total procedure - shorter than my current method of PCR purification.”
Marissa V. (Harvard Medical School)
“The elution volume is low enough to concentrate any sample very well and the efficiency is not compromised at all.”
Shanshan L. (UT Southwestern)
“This kit performed as described. I was able to obtain good quality and yield of the DNA -better than with a couple of competitor's kits.”
Kathleen B. (SUNY-ESF)
“The simple steps and washing instructions were excellent. DNA was ready for use for PCR and gave strong results.”
Tyler C.
Click here to submit your review of the DNA Clean & Concentrator™-5.

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