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Annealing temperature for oligos

Alan Kay kay at lyon151.inserm.fr
Wed Nov 22 05:08:53 EST 1995

Adela.Torres at uv.es (Adela Torres Calatayud) wrote:
>Hi everybody:
>I'm currently working on DNA non-radioactive cycle sequencing, and I'd like to 
>know if there is a reliable formula by which I can choose the annealing 
>temperature of the PCR program when I'm sequencing using custom-made oligos. 
>Right now the formula I'm using is:
>		2(A+T) + 4(G+C) - 6 = T ann.
>But it didn't give me good results when I tried it. So if there's anyone out 
>there that can help me, thanks very much! E-mail or post.
>					Adela Torres
>				         (Adela.Torres at uv.es)
The formula 2(A+T)+4(G+C)=Tm is OK for oligos less than 20-mers and at 1M salt, 
with annealing at 5-10° under Tm. For sequencing or PCR, salt concentrations 
are much less. For larger oligos or for taking into account salt concentration, 
I use the formula 81.5° + 16.6log(base10)M +o.41(%G+C) - 820/n, where M is the salt 
concentration in molar and n is the length of the oligo. In both editions of Maniatis, 
the formula is given as -16.6logM and 600/n. The first part is obviously wrong. U
nder 1M, the log becomes negative, and Tm diminishes with salt concentration. A
s for the length part, during site directed mutagenesis when I used differential 
hybridisation to distinguish between mutants and wild type, I found that the f
ormula I use is good to about 2°. However, I do all the hybridisations ot 6SSPE, w
hich is about 1M, so logM resolves to zero. If anyone has any good information a
bout the validity of formulae at lower salt concentrations, i.e. about 0.1M for P
CR, I would be glad to hear about it.


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