while i am performing 16sRNA amplification for streptomyces. the expected band is about 1000bp, but i got a band above 3000 bp? when i run the genomic DNA (native) on agarose gel i got a band at the same size equal to the pcr product (3000). what can i do?
I repeated the reaction with diluted DNA 1:10 the band disappeared?
it would be good to see a gel picture but it may be that you have dna (genomic) contamination at a level that you can see at normal concentration but is just too faint to see at 1/10 dilution. 3000 is too small but you may be using a concentration of agarose gel that just does not separate larger sizes of dna very well. If you really need to get rid of it perhaps rnase free dnase treatment but if it is well separated from your pcr product do you really need to get rid of it. Alternatively if you cannot see it at dilution then use the dilution and run a few more pcr cycles to get your productfor genomic dna
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