QIAGEN is cleaning up...DNA and RNA that is. With the addition of the DNeasy and RNeasy PowerClean Pro Cleanup Kits to our portfolio, we thought it would be a great time to discuss how cleanup kits work and when you'd want to use one. Clean-up kits take dirty nucleic acids and remove contaminants that could interfere with your downstream business. Enzyme-dependent applications like restriction digests, ligations, PCR amplification and sequencing all require squeaky clean DNA and RNA in order to get the best (or sometimes any!) results. Choosing the right clean-up kit for your needs depends on which substances you want to remove. Not sure? It depends on the source. Typically these reaction-killing interlopers are left over from either a previous enzymatic reaction or from the organism/environment that the DNA/RNA was extracted from. Our clean-up kits can be divided into two types based on which of these is the source of contamination.

 

Our fastest and simplest kits are those that are designed to remove proteins, primers, dNTPs and salts, typically left over after some kind of enzymatic reaction; for example, PCR amplification or a restriction digest. We have three different clean-up kits that will remove these simple proteins and salts; QIAquick PCR Purification Kit, QIAquick Gel Extraction Kit, and QIAEX II Gel Extraction Kit. If your DNA is suspended in solution you can use any of these. However, they do have some slight differences. Both QIAquick PCR Purification Kit and QIAquick Gel Extraction Kit are silica spin column-based kits. Consequently, they both have a DNA binding capacity of 10 micrograms per prep and they both will work with DNA up to 10 kb. QIAquick PCR Purification Kit will clean-up DNA of 100 bp – 10 kb, and QIAquick Gel Extraction Kit will cleanup DNA of 70 bp – 10 kb.

 

TheQIAEX II Gel Extraction Kit uses a silica suspension, instead of a spin column, to bind the DNA. This kit has a lower and upper DNA size limit of 40 bp – 50 kb. However, because the volume of silica can be increased or decreased as needed, it can be scaled for any quantity of DNA. The other advantage of QIAEX II Gel Extraction Kit is the option to elute the DNA in a small volume. So it is ideal if you want to concentrate your DNA as well as clean it up. The silica spin filter based kits have a minimum elution volume of 50 microliters.

 

In addition to DNA in solution, the QIAquick Gel Extraction Kit and QIAEX II Gel Extraction Kit also have protocols for cleaning up a DNA from an agarose gel. Since QIAEX II Gel Extraction Kit uses a silica suspension, it can accommodate any size slice of agarose gel. (Assuming you have a large enough collection tube!) On the other hand, the QIAquick Gel Extraction Kit should only be used with up to 400 mg of agarose, otherwise, it might clog the spin column.

 

But what if your dirty DNA/RNA sample contains contaminants other than just proteins, primers, and salts? Then you will need to take out the "big guns”! The DNeasy PowerClean Pro Cleanup and RNeasy PowerClean Pro Cleanup Kits work great for this. These kits feature streamlined protocols that enable DNA or RNA Cleanup in just 7 minutes. Inhibitors are removed using our Inhibitor Removal Technology (IRT) process for removing difficult substances that come from sources like plants, soil, feces or blood. Some common examples of contaminants, along with their typical sources are listed below:

 

• Humic acids (from soil, compost)

• Polysaccharides (plants, undigested contents in the rumen, ceacum, feces, drugs)

• Polyphenols (plants)

• Melanin (hair, skin, eye tissue)

• Bile salts (feces)

• Heme, EDTA, charcoal (blood)

 

Our original DNeasy PowerClean Cleanup Kit (Cat. No. 12877-50) is recommended for removal of inhibitors found in crude heparin and heparin products.

 

If you are trying to remove something not listed here and you are unsure if a DNeasy PowerClean Pro Cleanup or RNeasy PowerClean Pro Cleanup kit will work, please contact technical support. We might know the answer!

 

Find all this a bit confusing? The upshot is that any of our kits will remove proteins, primers, and salts. However, only those containing Inhibitor Removal Technology will remove environmental contaminants. We’ve put together a handy chart to make it a little easier to select the right kit for your needs. If you'd like to try our DNeasy or RNeasy PowerClean Pro Cleanup kits but aren't sure if it's right for you, contact customer service to order a free two prep kit: DNeasy PowerClean Pro Cleanup Sample (Cat. No. 12997-S) or RNeasy PowerClean Pro Cleanup Sample (Cat. No. 13997-S).

 

Cleaning up a lot of samples? We have two options available. The MagAttract PowerClean DNA Kit is a high-throughput, hands-free version of the DNeasy PowerClean Pro Cleanup Kit. It contains the same Inhibitor Removal Technology and ClearMag magnetic particle technology, enabling it to be run on a KingFisher Flex or Duo. The UltraClean 96 PCR Cleanup Kit is a high-throughput option that is similar to the QIAquick PCR Purification Kit. It includes a 96 well silica spin filter plate that is ideal for processing large numbers of samples without a robot.

 

Clean-up Kit

Binding matrix

Size range

Gel

Solution

Capacity

Inhibitors

Throughput

DNeasy PowerClean Pro Cleanup Kit

Silica Column

100 bp – 50 kb

 

X

20 ug

Environmental

Low

QIAquick PCR Purification Kit

Silica Column

100 bp – 10 kb

 

X

10 ug

Salts, proteins

Low

QIAquick Gel Extraction Kit

Silica Column

70 bp – 10 kb

X

X

10 ug

Salts, proteins

Low

QIAEX II Gel Extraction Kit

Silica suspension

40 bp – 50 kb

X

X

scalable

Salts, proteins

Low

RNeasy PowerClean Pro Cleanup Kit

Silica Column

100 bp – 50 kb

 

X

40 ug

Environmental

Low

UltraClean 96 PCR Cleanup Kit

Silica Column (plate)

60 bp – 10 kb

 

X

20 ug

Salts, protein

High

MagAttract PowerClean DNA Kit

ClearMag magnetic particles

60 bp – 50 kb

 

X

500 µg per 20 µl of beads

Environmental

High, hands-free