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If the primer is dimer,it's ok?


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5 replies to this topic

#1 kroger

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Posted 19 August 2004 - 03:45 PM

just place order in fisher oligos,and find information of one primer is dimer,is it ok?
thanks

#2 SVTX

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Posted 20 August 2004 - 08:07 PM

hi,
could you explain a little more about your problem...

SV

Edited by SVTX, 20 August 2004 - 08:07 PM.


#3 aj_xy999

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Posted 21 August 2004 - 12:10 AM

you have 2 choices:
1) either re-order your primer
or
2) perform the PCR with the primers & if you are not getting contaminating bands, don't worry.

#4 kant0008

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Posted 22 August 2004 - 09:56 PM

Hi,
I guess it depends on how much of the sequence dimerises. If it's a lot then you may not have any free primer for the PCR reaction to proceed, so you won't get a product.

#5 dinesh_nato

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Posted 23 August 2004 - 01:12 AM

You can use certain softwares (Primer Premier comes to mind ) that can give you the stability of the primer dimers. You can use this info to guess if the primer-dimers are going to be a factor since some primer-dimers are theoretically possible but in reality they have a hard time forming and maintaining dimers since the stability is low.

If time is not a factor in your experiment i would recommend that you try out the primers that you have allready ordered first before ordering a new one. Sometimes having primer-dimers aren't that bad , you can circumvent it by increasing the PCR temperature slightly to help destabilize the primer-dimers.

Good luck

#6 cytochrome

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Posted 23 August 2004 - 09:38 PM

Try hot-start PCR. Boil your reaction mixture for 5 to 10min before addition of Taq polymerase, then add your polymerase and do the PCR reaction. It might help. Should try to avoid forming primer dimer when design it, but this is not an absolutely dead situation.




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