DNA size markers

[Rina Carhuaz]

Dear friends:

I am running  SSR-PCR amplification products  by PAGE method using 100bp DNA 
marker (50ng/ul) as measure  of amplified DNA fragments size. In order to 
make sure the DNA fragments size was correct I added the 50 bp DNA marker 
 next to the other. However, when comparing the both marker bands (100 and 
50bp) I found no congruence of migrated distances  according the expected 
band size, ei. according 100bp marker,  a given PCR band measures 90bp 
 whereas according 50bp the same band measures 120bp. This situation became 
worst when a third marker (pUC19-MspI) was added.
Can anyone suggest me how to overcome this "fitless" marker band sizes and 
get them both congruent and reliable.
Thanks in advance for help.
Rina
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e-mail: rcarhuaz at cgnet.com
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