Annealing temperature of 10-mer oligo

[Terence]

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

[Ferland Louis H.]

Terence,

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
case).

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,

Louis

On 23 Feb 1996, Terence wrote:

> Date: 23 Feb 1996 04:18:38 GMT
> From: Terence <bcl...@uxmail.ust.hk>
> To: met...@net.bio.net
> Subject: Annealing temperature of 10-mer oligo

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

[Shaun Tyler]

Sure there are several quick methods for estimating annealing
temperature. The easiest is G/C = 4 C and A/T = 2 C. However,
regardless of the method you use, an "estimate" is all that you will get.
I hate to say it but if you need to be precise there is no alternitive
to imperical testing.

Shaun Tyler
DNA Core Facility
Laboratory Centre for Disease Control
Health Canada

Ph#: (613) 941-6441
FAX#: (613) 957-1358

E-mail: sty...@hpb.hwc.ca