HELP! Odd Gel Pattern!!

Shahram Mori smori at
Fri Jun 3 01:32:14 EST 1994

brunker at wrote:
:     Instead of getting descrete bands on our electrophoresed agarose gel, we've
: been getting "smeared" patterns...a dark band followed by a gradient of lighter
: stains trailing back to the well. (I hope I'm describing this clearly).
:     Does anyone know what causes this, and how we fix it? 
:     These are PCR products digested by Nco1, and should produce not more than
: three nice strips each, not counting the primer lines. The marker lane looks 
: fine. The pieces we're looking at (we hope) are ~30, ~190 and `160 pb's.
:     Has this happened to anyone else? Are we really producing an increasingly 
: large range of DNA strands? 
:     How could such a fate have befallen us?!!
:     Thanks,
:     Marla Brunker
:     brunker at
What maybe wrong is that your PCR was not specific enough and you have
gotten some non-specific amplified DNA.
Is your PCR from Genomic DNA? Do you have highly specific primers?
NCO1 may be cutting the contaminant amplified elements, thereby giving you
smearing. I know this sounds too weird but who knows.
Shahram Mori
Program in Molecular Biology 
Dept. of Chemistry and Biochemistry
NMSU Las Cruces NM 

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