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PCR product purification


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#1 albatross

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Posted 01 September 2009 - 07:41 AM

I often encounter a problem during PCR product purifications:

The desired fragment is always contaminated with small amount of unexpected fragment, particularly smaller ones.

For example, when I PCR amplified tDimer 2 gene which is about 1.4 kb, the purification pruduct is contaminated with a 0.7 kb fragment. This may because of the tandem repeat of tDimer 2 gene. However,
I found this problem happen a bit frequently when purify other PCR products.

Any consideration?

Thank you!

Edited by albatross, 01 September 2009 - 07:43 AM.


#2 almost a doctor

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Posted 01 September 2009 - 07:53 AM

I often encounter a problem during PCR product purifications:

The desired fragment is always contaminated with small amount of unexpected fragment, particularly smaller ones.

For example, when I PCR amplified tDimer 2 gene which is about 1.4 kb, the purification pruduct is contaminated with a 0.7 kb fragment. This may because of the tandem repeat of tDimer 2 gene. However,
I found this problem happen a bit frequently when purify other PCR products.

Any consideration?

Thank you!



How are you purifying your products? It'll be easier to suggest options if we know what you are doing.

#3 albatross

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Posted 03 September 2009 - 07:13 AM

I often encounter a problem during PCR product purifications:

The desired fragment is always contaminated with small amount of unexpected fragment, particularly smaller ones.

For example, when I PCR amplified tDimer 2 gene which is about 1.4 kb, the purification pruduct is contaminated with a 0.7 kb fragment. This may because of the tandem repeat of tDimer 2 gene. However,
I found this problem happen a bit frequently when purify other PCR products.

Any consideration?

Thank you!



How are you purifying your products? It'll be easier to suggest options if we know what you are doing.


I used the Qiagen purification kit.
Another problem is that i can not remove the primer dimer completely by gel purification even though the fragment is very large, 2.5 kb for example.

Edited by albatross, 03 September 2009 - 07:14 AM.


#4 gebirgsziege

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Posted 03 September 2009 - 07:38 AM

This used to be on protocol online.....
PEG purification

I only use this protocol, its easy robust, cheap and better than all kits I tried. Primer dimers are completely removed (but all fragments smaller than 200 bp as well!!!)
A man cannot be too careful in the choice of his enemies. (Oscar Wilde)




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