help! pcr of mtDNA control region

[Anderas Becker]

In article <40936m$nv2 at newsbf02.news.aol.com>, julia54601 at aol.com (Julia54601) says:
>
>Our lab has a strange result from the pcr of a 500 bp region that contains
>short repeat sequences.  Although we a pcr-ing from an isolated fragment,
>we are getting a heavy smear above the anticipated product.  Very large --
>right up to the wells.  We tried making the pcr more stringent and it
>won't go away.  Has anyone ever heard of repeat sequences acting as
>self-primers, sort of stringing products together?  Any advice or
>speculations?  Please send e-mail to my address:  Julia54601 at aol.com.  

Try other primers. MtDNA is highly repeated. Thats important for the disign of primers.
We created a program especially to avoid that problem.
We work on mtDNA too and had simular problems.
Try PrimerDesign to avoid it. You can find it at our side:

ftp://ftp.chemie.uni-marburg.de/PrimerDesign

or easier browse our www-site:

WWW  : http://www.chemie.uni-marburg.de/~becker

----------------------------------------------------------------------
Andreas Becker
Arbeitskreis Prof. Kadenbach, FB Chemie/Biochemie, Hans-
Meerwein-Strasse, Philipps-Universitaet, 35043 Marburg, Germany
Phone: privat +49 6421 47304  Labor +49 6421 28 -5721 Fax -2191
eMail: BECKER at ps1515.Chemie.Uni-Marburg.De