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DNA gel elctrophoresis problem

weirds dots

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#1 Bioscientist

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Posted 18 August 2014 - 02:21 PM

Hi everyone

 

In my gel electrophoresis I see some weird DNA zigzags. I ran the gel with PCR products and ladder. This problem is only visible at around 10-13 well no in the middle. The rest is fine. The tray and comb appears to be fine. The ladder is fine when run in different well. I haven't seen anything like this before. I have attached a photo of my gel. Any idea why that is happening? I have used fresh TAE buffer both for making the gel and as the running buffer.

 

Thanks!

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Edited by Bioscientist, 18 August 2014 - 02:22 PM.


#2 bob1

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Posted 18 August 2014 - 04:01 PM

I take it that this has happened only once?  If so - why worry about it.  It looks to me like you have some uneven gel pouring, perhaps some part that wasn't fully dissolved when poured.



#3 Bioscientist

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Posted 19 August 2014 - 06:38 AM

Thanks for the reply. But it happened thrice. The agarose completely dissolved and boiled a bit.



#4 Trof

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Posted 19 August 2014 - 07:12 AM

I see that sometimes too. It's some kind of dye smear. There is something which is absorbing more dye than the rest, there are probably many reasons why this may happen, not completely homogenous gel, not well stirred with the dye, some kind of different stuff inside the gel like salts or so, from the sample lines...who knows..

However it doesn't interfere with anything usually so I ignore it. And If I need a perfect gel picture, I take special care about the gel when I'm making it, boiling three times (but not to boil out too much water), cool with slowly stirring instead of "I don't have time for this, let's just cool it under the tap water", mix really well the EtBr inside, wipe out bubbles etc..  but usualy you just need to see bands, I don't worry about it at all.


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