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Primer extension problem - there are too many bands!! (Aug/26/2005 )

I have a difficulty to find out the transcriptional start point of a E.coli gene by primer extension.
There is no disticnt band, but a set of bands all over the sequencing gel, as in DNase footprinting. mad.gif mad.gif mad.gif
Whan can i do to improve this?

Please help.


It could mean multiple transcriptional start sites (TSS) or non-specific binding. Make sure your RNA is not degraded by checking it using gel analysis. Your primer should be at least 20 mer in length, binds at a position at least 100 bp downstream the TSS, has no significant homology with other mRNA sequences.