Biotin Pcr primers and anealing temperature

John Dixon jpcd0 at
Thu Aug 22 12:59:09 EST 1996

In article <4vi08d$blo at>, karl at
(Karl Voss) wrote:

> Hi,
> Does anyone know if having 5' biotin on pcr primers lowers the anealing 
> temperature that they need.  I have been getting very good pcr results with
> a non-biotinilated primer set that have short 5' sequence overhangs to be
> used for directional cloning.  I wanted to directly sequence the pcrs so 
> I got a biotinilated primer made that did not have the extra 5' bases.
> The resulting pcr bands are very weak.  I have quantified the primers 
> carefully and assume that they are of high purity (they were purchased from 
> Research Genetics).
> Has anyone run into similar situations?  If so I would like to hear
> from you.

Hi Karl, I have just made a biotinylated primer that exactly matches a
primer made for somebody in the lab 5 years ago that still works fine. The
new biotinylated one completely fails, even on pure plasmid, while the old
one PCRs from the genome (mouse) no worries. I am in the process of
complaining to the oligo service but the spec analysis looked fine. I have
to say that I have only tested the new one uneder the exact conditions
used for the old, so that if the annealing temperature has changed
dramatically, this might explain it some of the problem.

cheers, John

John Dixon                                        Lab 44 (1223) 334131
Wellcome/CRC Institute                            Fax 44 (1223) 334134
Department of Genetics
Cambridge University    
United Kingdom                           e-m: jpcd0 at

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