Primer Design

Michael Morales mmorales at acpub.duke.edu
Tue Feb 4 12:26:39 EST 1997


: Mirna Perez (mperez at FISIO.CINVESTAV.MX) wrote:
: : Hi!

: : I design an oligonucleotide for a PCR reaction, but I am not sure if its
: : lenght is enough (14bp) to performance a reaction. The oligo contains
: : 12G/C and 2A/T, and its Tm is high (80"C). Is it lenght good enough to
: : do a PCR reaction?
: : 			Thanks

Mirna, 

With that many G/Cs I would be very worried about the possibility of very 
stable secondary structures forming within the oligo, which would prevent it 
from annealing to your template.

Good luck, hope this helps,

Mike Morales   


: : 			 Mirn

: i am afraid it may not be long enough tobe really specific,
:  unless the DNA template is so pure that you are sure there is
: n  othing else to amplifye! A quick way to test your primers
:  is to screen Genbank with them. Also I think it is better
:  to have a G/C  content closer to 50%
: Good luck. Let me know the result of the search through databank.
: Natalie.



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