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problem with optimized protocol - (May/25/2007 )

hi everyone
i have optimized a PCR for a gene it gave really good results with different samples but now i m facing a big problem that when i used do the PCR reaction with the same conditions i get the smear instead of a proper band of DNA, i have already changed my Primer dilution twice, buffer, Taq polymerase enzyme, dNTPs, water but i m getting the same results even i have tried to re-amplify the PCR which i get positive there there was a clear band but again there is only smear.
i m very worried about it because i have to submit a report to my supervisor as soon as possible, can any one help me in this regard
saba

-sabahat Khaliq-

Try diluting your template 10x and 100x.

-phage434-

I assume that your DNA template is genomic DNA.

another thing you should do is run some of your uncut template DNA out on a 1% agarose gel. This is to check that your DNA is still in good shape and have not yet degraded.l

If the DNA is good, it should form a high molecular weight band with little or no downward streaking. The more downward streaking, the more low molecular weight DNA is present, and thus the more degraded the DNA is.

-perneseblue-

QUOTE (sabahat Khaliq @ May 25 2007, 09:50 PM)
hi everyone
i have optimized a PCR for a gene it gave really good results with different samples but now i m facing a big problem that when i used do the PCR reaction with the same conditions i get the smear instead of a proper band of DNA, i have already changed my Primer dilution twice, buffer, Taq polymerase enzyme, dNTPs, water but i m getting the same results even i have tried to re-amplify the PCR which i get positive there there was a clear band but again there is only smear.
i m very worried about it because i have to submit a report to my supervisor as soon as possible, can any one help me in this regard
saba


i think may be your pcr machine may have a problem....
try to use different machine or set up a gradient PCR....once

all the best

-HHHH-