Any real difference between DNA purification kits? - (May/02/2014 )

Is there any important difference between e.g. PCR clean-up, eukaryotic genomic DNA extraction, mini-, midi-, maxi- plasmid prep, gel extraction kits sold by different companies or are they all selling the same things?

There is a difference between genomic DNA preparation kits and plasmid preparation kits. The kits for PCR cleanup, gel purification, and column based plasmid kits are pretty similar in the final portion of the protocols, but differ in the sample handling early on, primarily in releasing the DNA and adjusting chemistry so that it binds. The charge-switch kits are different chemistry. I'm now a fan of magnetic bead purification for most applications.

I'm not sure whether my question was clear. Just in case, I'm asking whether there's a difference between the kits of different companies' (e.g. QIAGENs vs Promegas vs Life Technologies) kits.

 

Why do you prefer magnetic bead-based kits? Have you been using them long?

In general there isn't much difference, though there may well be some adjustment of the chemistry to enhance DNA extraction over the basic protocols, though these bits would be proprietary (check the MSDS they will often tell you components based on hazard).

The costs make sometimes the difference .

 

For DNA extraction kits I know a study where they compared several kits to extract DNA from museum species and they found quite clear differences between companies in terms of DNA yield and PCRs with this DNA (working or not). Therefore especially for difficult and unusual sources the differences can be huge, whereas for standard samples the differences might be small (and differences in results due to differently skilled users can superimpose the actual kit differences).

Generaly QIAGEN is thought to be the best, and also the most expensive (may not be true at different uses and needs, both of these).

 

For PCR cleanup/gel extraction, I don't know about the others, but Q offers colums with minimal elution volumes, which makes DNA isolated from gel to have reasonable concentration for spectrophotometric measuring (i.e. more than 10 ng/ul). Any other companies, may have half the prize for column kit, but half the yield and much bigger elution volume, so at the end you get so low concentration it's hard to measure.

 

For plasmids, there depends how much you care about yield. Minipreps are usually only good for testing, and you do a lot of them so we use column kits from a noname cheep company (but we don't use their gel extraction kits as I mentioned). In this case, prize is more important.

Q has even several types of isolation for Midi and Maxi preps, some use filter, some not (in one case needs a centrifuge force we didn't have, so we ended using several midipreps instead of Maxi, when only overall yeald is required and not a high concentration, because it was both cheaper and more bothersome). But if you cultivate a huge bottle of bacteria, you don't want to waste it on some shitty cheap kit. 

 

Genomic DNA isolation depends much on the type of source tissue and how much you want do bother with it. Q has really many types, for lipidous tissues, plants, etc, many protocols. You can use a whole blood if you want, but as I'm a "blood person" I still prefer classic phenol/chlorophorm, because there is generaly no kit, that would process 6-9 ml of whole blood, the colum kits are usualy up to 1 ml, that's a waste..  but fine for small animals blood, where you don't have that much and you need a PCR-grade DNA.

 

And.. several companies have differen systems, Q has mostly columns, but few other types, and those kits for the robot of theirs, also column kits that are compatible with vacuum thingy they sell.

Other companies have magnetic beads (not sure if Q makes them) so if you prefer certain type, you choose a company by that. (some other company was really into some weird filtering stuff, for isolations, there are many approches).

 

LifeTech engulfed Invitrogen and late Ambion, and Ambion was known for the best RNA stuff. But RNA is more tricky thing than DNA. RNA isolation kits we use are mostly not from Q. So, depends on who is doing the best, the exact thing you need. 

 

 

But personally I found another huge plus for Q, in theyr marvelous protocols. There just the small books you can read, some background info, clear and comprehensible protocol (protocol variants often).. I've seen Invitrogen manuals, Promega manuals (my god..), ABI manuals (they are so full of safety nonsense and whant other things you should buy from them..), I have seem folded papers of noname companies, but QIAGEN simply makes the best manuals. 
I would take it as a reading on a vacation, with graphs and pictures!

No seriously, I found the comfort of work also an important part. Sometimes it's worth the money, sometimes not.

 

There is also this company that sells alegedly "the same colums as QIAGEN has" in bulk and manual how to mix your own "QIAGEN" buffers. That is also possible. 

Trof on Tue May 6 21:13:28 2014 said:

Generaly QIAGEN is thought to be the best, and also the most expensive (may not be true at different uses and needs, both of these).

 

For PCR cleanup/gel extraction, I don't know about the others, but Q offers colums with minimal elution volumes, which makes DNA isolated from gel to have reasonable concentration for spectrophotometric measuring (i.e. more than 10 ng/ul). Any other companies, may have half the prize for column kit, but half the yield and much bigger elution volume, so at the end you get so low concentration it's hard to measure.

 

For plasmids, there depends how much you care about yield. Minipreps are usually only good for testing, and you do a lot of them so we use column kits from a noname cheep company (but we don't use their gel extraction kits as I mentioned). In this case, prize is more important.

Q has even several types of isolation for Midi and Maxi preps, some use filter, some not (in one case needs a centrifuge force we didn't have, so we ended using several midipreps instead of Maxi, when only overall yeald is required and not a high concentration, because it was both cheaper and more bothersome). But if you cultivate a huge bottle of bacteria, you don't want to waste it on some shitty cheap kit. 

 

Genomic DNA isolation depends much on the type of source tissue and how much you want do bother with it. Q has really many types, for lipidous tissues, plants, etc, many protocols. You can use a whole blood if you want, but as I'm a "blood person" I still prefer classic phenol/chlorophorm, because there is generaly no kit, that would process 6-9 ml of whole blood, the colum kits are usualy up to 1 ml, that's a waste..  but fine for small animals blood, where you don't have that much and you need a PCR-grade DNA.

 

And.. several companies have differen systems, Q has mostly columns, but few other types, and those kits for the robot of theirs, also column kits that are compatible with vacuum thingy they sell.

Other companies have magnetic beads (not sure if Q makes them) so if you prefer certain type, you choose a company by that. (some other company was really into some weird filtering stuff, for isolations, there are many approches).

 

LifeTech engulfed Invitrogen and late Ambion, and Ambion was known for the best RNA stuff. But RNA is more tricky thing than DNA. RNA isolation kits we use are mostly not from Q. So, depends on who is doing the best, the exact thing you need. 

 

 

But personally I found another huge plus for Q, in theyr marvelous protocols. There just the small books you can read, some background info, clear and comprehensible protocol (protocol variants often).. I've seen Invitrogen manuals, Promega manuals (my god..), ABI manuals (they are so full of safety nonsense and whant other things you should buy from them..), I have seem folded papers of noname companies, but QIAGEN simply makes the best manuals. 
I would take it as a reading on a vacation, with graphs and pictures!

No seriously, I found the comfort of work also an important part. Sometimes it's worth the money, sometimes not.

 

There is also this company that sells alegedly "the same colums as QIAGEN has" in bulk and manual how to mix your own "QIAGEN" buffers. That is also possible. 

 

Now I'm wondering if you have a contract with the "Q" company?

Maybe for people working with "clean" stuff QIAGEN is a reference. For the ones we work in environmental micro, you never use their kits for isolation. Probably, MoBIO has more stuff in environmental DNA extraction than any other company. And if you use kits for that type of samples you usually use either one from MOBIO or the FastDNA Spin kit (or one the many protocols derived from it).

hobglobin on Wed May 7 16:40:31 2014 said:

Now I'm wondering if you have a contract with the "Q" company?

No, but I obviously should ask them to 
 
(they're are expensive, so not an option for everyone, but as said, often a "golden standard")
 
 
 

El Crazy Xabi on Thu May 8 05:39:16 2014 said:

Maybe for people working with "clean" stuff QIAGEN is a reference. For the ones we work in environmental micro, you never use their kits for isolation. Probably, MoBIO has more stuff in environmental DNA extraction than any other company. And if you use kits for that type of samples you usually use either one from MOBIO or the FastDNA Spin kit (or one the many protocols derived from it).

Didn't they have that miraculous polymerase mixes, that can overcome many inhibitors? One company had such, especially for soil samples and other.. so you could do onsite PCR (but I don't remember which company that was). I found that very interesting, but I don't need that actually.

Q supplies "Q solution" which is 1M betaine.  They forgot to pay me this month... ;-)