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-   -   no band observed for genomic DNA during agarose gel electrophoresis (http://www.molecularstation.com/forum/agarose-gel-electrophoresis-forum/47786-no-band-observed-genomic-dna-during-agarose-gel-electrophoresis.html)

syoke_85 12-17-2008 01:46 AM

no band observed for genomic DNA during agarose gel electrophoresis
 
i have extract the DNA from food sample.Once i run the gel electrophoresis for genomic DNA,there is no band observed. But under UV light, there exists orange color in the well of the gel. is it the DNA stuck in the well and cannot be seperated out? or the size of DNA is too big for it to be seperated?
can someone help me to settle this problem? thanks!

butters 12-17-2008 02:37 AM

Re: no band observed for genomic DNA during agarose gel electrophoresis
 
what is the amount of DNA detect by spectro? what percent of gel are u running? 1% would be good for gDNA electrophoresis.

syoke_85 12-17-2008 10:26 AM

Re: no band observed for genomic DNA during agarose gel electrophoresis
 
thanks for the reply...
i have tried out 1% and also 1.5% agarose gel..and i am using 80 volt for 1 hr to run the gel, bt there is no band at all! is it the voltage or time problem?
i did not quantify the amount of DNA using spectrophotometer since i just wanna confirmed the existence of genomic DNA in food samples...
is someone having the same problem as me?

Aga 12-17-2008 04:10 PM

Re: no band observed for genomic DNA during agarose gel electrophoresis
 
So the thing is that you either have too long DNA fragment so it doesn't seem to migrate during the time you run electrophoresis for or you don't have DNA at all.
I isolated DNA from food samples. Since food is a complex mixture of different ingredients I had different DNA fragments isolated. After loading my samples onto a gel I had different size DNA fragments similar to a smear. I run it in 0.8% agarose gel.

Pay attention to the fact that the smear - like picture I had resulted from the fact that I isolated DNA from processed food, so some DNA were degraded due to processing and I had shorter fragments.

Do yo have any access to spectrophotometer? You can analyse DNA content using the wave lenght of 260nm.
If you have spectrophotometer linked to a computer with proper software it will be easier - you will obtain the result as a peak - for DNA it is a peak for 260 nm. If you don't have the software you have to check the absorbance for 260nm, 280nm and 320nm (to check the purity). I'm sure you will find more answers searching the net, but if not I'll write more about it.

If you have cuvette spectrophotometer you will have to dilute your DNA sample so take it into consideration. Nanodrop is better in this situation - you need only 2 microliters of sample.

If the result shows very little absorbance for 260nm wave lenght then probably you didn't extract the DNA from your food samples. This may mean that orange fluorescence on the gel comes from some protein-like compounds or complexes.

sweet_sarmi 11-20-2010 02:33 AM

Re: no band observed for genomic DNA during agarose gel electrophoresis
 
hiiii... even i am facing the same problem though i have checked the OD of the DNA in a spectrophotometer and it seems to be in the range only means in between 1.7- 1.9. then what can be the reason behind this?

admin 12-22-2010 01:38 PM

Re: no band observed for genomic DNA during agarose gel electrophoresis
 
I often had this issue for genomic DNA.

To see the genomic DNA You have to run the gel for a LONG time, and make very fragile low agarose gels to separate out the genomic DNA through the gel.

You can run 0.3% gels to see Genomic DNA, anything over 0.6% and you will hardly get separation and if you do it will take a long time to see the DNA get into the gel much

see this great article for more:

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