QIAEX II System Gel Extraction Kit

For purification of DNA fragments (40 bp to 50 kb) from gels and solutions


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QIAEX II Gel Extraction Kit (150)

Cat. No. / ID:  20021

For 150 extractions: 3 x 0.5 ml QIAEX II Suspension, Buffers
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The QIAEX II System is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

✓ 24/7 automatic processing of online orders

✓ Knowledgeable and professional Product & Technical Support

✓ Fast and reliable (re)-ordering


  • Efficient extraction of DNA from 40 bp to 50 kb
  • Gel extraction from TAE or TBE agarose gels and polyacrylamide gels
  • No sodium iodide to interfere with subsequent reactions
  • No shearing of large DNA fragments

Product Details

The QIAEX II system provides a suspension of silica particles to which DNA fragments bind in the presence of chaotropic salts. QIAEX II Suspension is added to solutions or solubilized agarose gel slices and binds DNA. The particles are collected by a brief centrifugation, washed and DNA of 40 bp to 50 kb is eluted in Tris buffer or water.


Using the QIAEX II system, 10 ng to 10 µg DNA are recovered efficiently (see figure  "Consistent recovery"). The versatile procedure for batch purification of gel fragments can be easily scaled up to a binding capacity of 15 µg using 30 µl QIAEX II suspension.

The QIAEX II system provides silica particles for purifying 60–95% DNA fragments (40 bp – 50 kb). A volume of 10 µl QIAEX II suspension binds up to 5 µg DNA, which is subsequently eluted in 20 µl.

Recovery according to size

DNA size Recovery, percent*
44 bp 75
75 bp 75
500 bp 95
7.5 kb 85
23.5 kb 75
48.5 kb 60
See figures


Purification of DNA fragments with the QIAEX II system is based on solubilization of agarose and selective adsorption of nucleic acids onto QIAEX II silica-gel particles in the presence of chaotropic salt. QIAEX II separates DNA from salts, agarose, polyacrylamide, dyes, proteins and nucleotides without phenol extraction or ethanol precipitation. QIAEX II is effective for any type of agarose in either TAE or TBE buffers.

QIAEX II particles provide a slurry for gel extraction and ensure efficient recovery without shearing, even for large DNA fragments. Optimized buffers permit DNA recovery without sodium iodide, which is difficult to remove from DNA samples, and may affect subsequent reactions.

The solubilization and binding buffer used with the QIAEX II system contains a unique pH indicator. A simple color change indicates whether the pH of the binding mixture is optimal for efficient adsorption of DNA to QIAEX II silica particles (see figure  "pH indicator dye"). The colored dye also allows easy visualization of any unsolubilized agarose in the binding mixture, ensuring complete solubilization for maximum yield.

pH indicator dye in the solubilization and binding buffer allows easy visual determination of optimal pH for DNA adsorption (pH ≤7.5). An incorrect binding-mixture pH can occur if the agarose gel electrophoresis buffer was frequently used or incorrectly prepared. In this case the pH can be easily adjusted by addition of 10 µl 3 M sodium acetate, pH 5.0.

See figures


QIAEX II silica-gel particles are added to the solubilized gel slice, and the particles collected by a brief centrifugation step (see flowchart  "QIAEX II procedure"). After washing, the pure DNA fragment is eluted in 20 µl of Tris buffer or water.

The QIAEX II system provides QIAEX II suspension together with binding and wash buffers, and a comprehensive handbook. Protocols are provided for purification of DNA from agarose gels, solutions and polyacrylamide gels.

See figures


DNA purified with the QIAEX II system can be used directly in most applications, including:

  • Restriction digestion
  • Labeling
  • Ligation
  • PCR

Features Specifications
Binding capacity 5 µg/10 µl
Elution volume 20 µl
Format Tube
Fragment size 40 bp – 50 kb
Processing Manual
Recovery: oligonucleotides dsDNA Recovery: dsDNA fragments
Removal <10mers 17–40mers dye terminator proteins Removal <40mers
Sample type: applications DNA: PCR reactions
Technology Silica technology

Supporting data and figures


Kit Handbooks (1)
Safety Data Sheets (1)
Quick-Start Protocols (1)
Certificates of Analysis (1)


T-B+NK+ severe combined immunodeficiency caused by complete deficiency of the CD3zeta subunit of the T-cell antigen receptor complex.
Roberts JL; Lauritsen JP; Cooney M; Parrott RE; Sajaroff EO; Win CM; Keller MD; Carpenter JH; Carabana J; Krangel MS; Sarzotti M; Zhong XP; Wiest DL; Buckley RH;
Blood; 2006; 109 (8):3198-206 2006 Dec 14 PMID:17170122
Role for nonstructural protein 1 of severe acute respiratory syndrome coronavirus in chemokine dysregulation.
Law AH; Lee DC; Cheung BK; Yim HC; Lau AS;
J Virol; 2006; 81 (1):416-22 2006 Oct 11 PMID:17035307
Effects of the chemotherapeutic agent doxorubicin on the protein C anticoagulant pathway.
Woodley-Cook J; Shin LY; Swystun L; Caruso S; Beaudin S; Liaw PC;
Mol Cancer Ther; 2006; 5 (12):3303-11 2006 Dec PMID:17172434
Exportin-5 orthologues are functionally divergent among species.
Shibata S; Sasaki M; Miki T; Shimamoto A; Furuichi Y; Katahira J; Yoneda Y;
Nucleic Acids Res; 2006; 34 (17):4711-21 2006 Sep 8 PMID:16963774


I bound an 11 kb DNA fragment to a QIAquick column; is it completely lost?

Larger DNA fragments bind more tightly to the QIAquick columns. It is difficult to predict whether a DNA fragment larger than 10 kb can be efficiently recovered, because this depends on base composition as well as fragment size. If the fragment is only a few kb larger than the 10 kb limit, it can be helpful to heat the elution buffer EB to 60°C and let it incubate on the column for a few minutes before centrifuging. However, please note that it will become less likely to recover your sample the larger the fragment size is. As we cannot guarantee recovery of fragments larger than the maximum cutoff size, we do not recommend to purify such fragments using QIAquick Kits.

The QIAEX II Kit can be used to extract DNA fragments up to 50 kb from agarose or polyacrylamide gels.


FAQ ID -756
How can I improve ligation efficiency of DNA from a QIAEX II Gel Extraction Kit?
Assuming that the ligation conditions are correct, QIAEX II particle carryover may affect ligation efficiency. Under low salt conditions, enzymes may bind to QIAEX II particles, thus reducing enzymatic activity in the ligation reaction. To remove the particles, centrifuge the tube containing the DNA for 30 seconds before pipetting the DNA.
FAQ ID -141
Can I store agarose gel slices containing DNA for gel extraction at a later point?
Cut out the slice of agarose containing the DNA fragment of interest, and store it at 4oC in an Eppendorf tube sealed with Parafilm.
FAQ ID -313
Is it possible to isolate single stranded DNA (ssDNA) with the QIAEX II Kit from agarose or polyacrylamide gels?
Yes, single stranded DNA can be isolated from agarose or polyacrylamide gels using the QIAEX II Gel Extraction Kit.
FAQ ID -576
Why does my DNA sample float out of the slot when loading it onto an agarose gel?

DNA fragments purified with the QIAGEN DNA Cleanup Systems, i.e., the QIAquick PCR Purification Kit, the MinElute Reaction Cleanup Kit, the QIAEX II Gel Extraction Kit etc. may float out of the loading wells of agarose gels due to residual ethanol carried over from the wash step with Buffer PE (despite the addtition of glycerol-containing loading buffer).

Use either of the following options to remove residual ethanol from the eluate:

  • re-purify the sample using a QIAquick-, or MinElute column, or QIAEX II resin
  • incubate the eluate at 56°C for 10 min to evaporate the ethanol
  • dry down the sample in a vacuum centrifuge, and resuspend the pellet in a small volume of sterile water
FAQ ID -205
Is it possible to clean up a methylation reaction containing bisulfite with QIAquick Cleanup Kits?
Yes, bisulfite containing methylation reactions can be cleaned up with our silica-based cleanup products, such as QIAquick and QIAEX II. Please see Goyon et al. (1994),  'Perpetuation of cytosine methylation in Ascobolus immersus implies a novel type of maintenance methylase', published in J Mol Biol. 1994 Jul 1;240(1):42-51, for a reference.
FAQ ID -519
What is the small band below my fragment of interest on an agarose gel after DNA cleanup using QIAquick?

Occasionally, DNA fragments eluted from the silica matrix of QIAquick, MinElute or QIAEX II Kits will contain denatured single-stranded DNA (ssDNA), appearing as a smaller band on an analytical gel. Under certain conditions, chaotropic agents (present in all silica-based DNA purification methods) can denature DNA fragments. This is a rare event that may be influenced by sequence characteristics such as the presence of inverted repeats or A–T-rich stretches.

Because salt and buffering agents promote renaturation of DNA strands, the following tips are recommended:

  • use the eluted DNA to prepare your downstream enzymatic reaction, but omit the enzyme. Incubate the reaction mix at 95°C for 2 minutes to reanneal the ssDNA, and allow the tube to cool slowly to room temperature before adding the enzyme and proceeding
  • alternatively, the DNA can be eluted from the silica-gel membrane or resin in 10 mM Tris buffer containing 10 mM NaCl. However, the salt concentration of the eluate must then be taken into consideration in downstream applications.
FAQ ID -148
How can I extract DNA from a polyacrylamide (PAGE) gel?

The QIAEX II and QIAquick Gel Extraction Kit can be used to extract DNA from polyacrylamide gels.

The QIAEX II Handbook contains a protocol for Polyacrylamide Gel Extraction. A specialized User-Developed Protocol (QQ05) is available when using the QIAquick Gel Extraction Kit for this purpose.

Both protocols require the preparation of a diffusion buffer and a disposable plastic column or syringe barrel containing a Whatman GF/C filter or siliconized glass wool. To ensure optimal diffusion, cut the gel slices as small as possible, and use 2 volumes of diffusion buffer per 1 volume of gel. Increasing incubation time (protocol step 3) may result in higher yields.

FAQ ID -120