Annealing temperature of 10-mer oligo

Ferland Louis H. ferlandl at ERE.UMontreal.CA
Fri Feb 23 07:03:50 EST 1996


The rule of thumb to estimate the Tm of an oligo is: count 2 C for each A 
or T and 4 C for each G or C. However, this is usually considered valid 
for oligos between 15 and 30 nt in length. Very short oligos seem to be able 
to stick somewhat better than would be thus calculated: consider random 
priming reactions using hexamers (at room temp): you would need pretty 
much all G and C just to reach rT (6 X 4 = 24 C), yet all hexamers are 
supposed to prime (though I'm not positive that this is actually the 

For your 10-mer, try annealing conditions used in random priming 
protocols. If 6-mers can stick, your 10-mer should too.

Hope this helps,


On 23 Feb 1996, Terence wrote:

> Date: 23 Feb 1996 04:18:38 GMT
> From: Terence <bclong at>
> To: methods at
> Subject: Annealing temperature of 10-mer oligo
> 	Is there any quick method to estimate the annealing temperature 
> of a DNA oligomer as short as 10 bases to its template? Assuming it is
> a perfect match. I recalled that there is some formular for this but it
> seems that it may not be applicable to oligomer of this length. Thanks.
> Terence

Dr. Louis H. Ferland
Centre de Recherche, Hotel-Dieu de Montreal
Dept de Nutrition, Universite de Montreal
Phone: (514) 843-2757     FAX: (514) 843-2719

More information about the Methods mailing list