Zymoclean™ Gel DNA Recovery Kit

Quick (15 minute) recovery of ultra-pure DNA from agarose gels.
Column design permits DNA elution at high concentrations into minimal volumes (≥ 6 µl).
Eluted DNA is well suited for use in DNA ligation, sequencing, labeling, PCR, etc.

Product Size Catalog # Price Qty
Zymoclean™ Gel DNA Recovery Kit 10 Preps D4001T
$25.00
Zymoclean™ Gel DNA Recovery Kit - Uncapped columns 50 Preps D4001
$85.00
Zymoclean™ Gel DNA Recovery Kit - Uncapped columns 200 Preps D4002
$306.00
Zymoclean™ Gel DNA Recovery Kit - Capped columns 50 Preps D4007
$85.00
Zymoclean™ Gel DNA Recovery Kit - Capped columns 200 Preps D4008
$306.00

About Zymoclean™ Gel DNA Recovery Kit

The Zymoclean™ Gel DNA Recovery Kit provides for the rapid purification of high quality DNA from TAE/TBE-buffered agarose gels. The product features Fast-Spin technology to yield high-quality, purified DNA in just minutes. DNA purified using the Zymoclean™ Gel DNA Recovery kit are perfectly suited for use in DNA ligation reactions, sequencing, DNA labeling reactions, PCR, etc.


Format Spin Column
DNA Recovery Typically, up to 5 µg total DNA per column can be eluted with ≥6 µl water. For DNA 50 bp to 10 kb the recovery is 70-90%. For DNA 11 kb to 23 kb the recovery is 50-70%.
Processing Time 15 min
Equipment Microcentrifuge
DNA Size Limits 50 bp to 23 kb
Sample Sources DNA excised from TAE/TBE-buffered agarose gels.
DNA Purity High quality, purified DNA is eluted with water which is especially well suited for sequencing, ligation reactions, PCR, labeling, and restriction endonuclease digestions.
Product Detergent Tolerance ≤5% Triton X-100, ≤5% Tween-20, ≤5% Sarkosyl, ≤0.1% SDS

   

DNA fragments recovered from an agarose gel using the Zymoclean™ Gel DNA Recovery Kit. Lanes: M: DNA Ladder; 1-5: individual ladder DNA fragments.

DNA sequencing chromoatogram of a PCR product recovered using the Zymoclean™ Gel DNA Recovery Kit. DNA was recovered from a 2% (w/v) agarose gel and used directly for sequencing.

Step 1

Excise the DNA fragment1 from the agarose gel using a razor blade, scalpel or other device and transfer it into a 1.5 ml microcentrifuge tube.

Step 2

Add 3 volumes of ADB to each volume of agarose excised from the gel (e.g. for 100 µl (mg) of agarose gel slice add 300 µl of ADB).

Step 3

Incubate at 37-55 °C for 5-10 minutes until the gel slice is completely dissolved2.

For DNA fragments > 8 kb, following the incubation step, add one additional volume (equal to that of the gel slice) of water to the mixture for better DNA recovery (e.g., 100 µl agarose, 300 µl ADB, and 100 µl water).

Step 4

Transfer the melted agarose solution to a Zymo-Spin™ Column in a Collection Tube.

Step 5

Centrifuge for 30-60 seconds.  Discard the flow-through3.

Step 6

Add 200 µl of DNA Wash Buffer to the column and centrifuge for 30 seconds.  Discard the flow-through.  Repeat the wash step.

Step 7

Add ≥ 6 µl DNA Elution Buffer4 or water5 directly to the column matrix. Place column into a 1.5 ml tube and centrifuge for 30-60 seconds to elute DNA.

Ultra-pure DNA is now ready for use.

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

Product FAQs

  • The ADB we received is clear/yellow and now it is yellow/clear? Is it a pH indicator in the buffer similar to other kits? Has the buffer formulation changed? I feel that it has affected my purifications.

    The color is due of the oxidation of NaI that is in the buffer (clear to yellow). It will not affect the performance of the buffer. It is not a pH indicator.

  • What is the maximum weight of gel slice I can use? Should I use more ADB for higher % gels?

    Up to 400 mg of agarose. (1.6 ml sample with ADB).  Add 4 volumes for agarose gels >2% and ensure the gel silce has been fully dissolved prior to proceeding to the next step.

  • I'm getting low recovery

    Ensure Agarose is Fully Dissolved

    There may be small globules of undissolved agarose in the sample that can interfere with DNA recovery by clogging the column and leeching salts into the eluate. 

    Gel Dissolved at Temperatures Above 60 °C

    If dissolved at a higher temperature, DNA may be denatured affecting recovery.  For optimal results, dissolve the gel slice between 37-55 °C.

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

    Incomplete Elution

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

  • I'm getting a low A260/A230 ratio

    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 a low A260/A230 ratio.  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 (see below).

  • Following Clean-up, 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.

  • General Zymoclean Tips

    1)  Ensure that all of your 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.

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Featured Citations

Anaerobic bacterial strains from Antartica were sequenced for phylogenetic analysis and molecular studies revealed the possibility of a novel genus and species using 16S rRNA sequence and the recA gene. The Zymoclean™ Gel DNA Recovery Kit was used to gel purify recA PCR bands to ensure successful amplification.
The Zymoclean™ Gel DNA Recovery Kit was used to purify Cytochrome P450 (CYP) encoding PCR products and was followed by cloning in a yeast expression vector for CYP production. Researchers reported new CYPs involved in the synthesis of phytoalexins, antimicrobial toxins against plant pathogens.
The Zymoclean™ Gel DNA Recovery Kit was used to recover PCR products, which was then used in high-throughput sequencing to elucidate epigenetic variables and sequences to improve CRISPR-Cas9 genome targeting and editing. An in-vivo library-on-library approach was utilized for the simultaneous assessment of single guide RNA activity across 1,400 genes from various bacterial species.
High quality DNA was purified using the Zymoclean™ Gel DNA Recovery Kit for the purpose of the heterologous expression of a pleiotropic drug resistance transporter in E. coli. This innovation outlines a process of discovery and validation of fungicide resistance genes and highlights the potential for multidrug resistance in Sderotinia homoeocarpa.
The unique ability of the Zymoclean™ Gel DNA Recovery kit to efficiently recover high DNA yields contributed to the development of a novel method for high quality, next-generation sequencing library preparation. Zymoclean was employed for robust recovery of picogram amounts of DNA from agarose gels. Sequencing and subsequent analysis of the library demonstrated that the library had near-complete coverage of the mouse genome (Parkinson et al, 2011).

“I had tried three other kits to do a certain recovery before this, I was getting bad yields, the elution volume required was quite large, the protocols were not as easy to follow and they took longer to complete. I liked everything about this kit, it is simple, efficient and quick. The protocol is easy to follow and the yield was 4-5 times better than what I got from other kits.”
Wendy P. (University of Auckland)
“Protocols are very well written and Instructions easy to follow. Always had good results with your products.”
Simin H. (University of California, Irvine)
“The kit was very easy to follow and yielded good results. It was more affordable than the Qiagen Gel Extraction kits, but worked just as efficiently. Solid product“
Thomas B (University of Tennessee, Knoxville)
“The ADB buffer and higher temperature used melted the gel quicker than previously used kits thus making DNA recovery using this kit more efficient and generally quicker than previously used kits.”
Kelly-Anne F.
“The best advantage about this kit is that it is really quick to make it, and the total DNA recuperated have a good quality and it have a good concentration to follow the experiments.”
Ingrid M.
Click here to submit your review of the Zymoclean™ Gel DNA Recovery Kit.

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