Gel Smiling

Sui Huang suihuang at usa1.com
Sat Sep 30 13:43:01 EST 1995


In article <44g2b7$6nc at Twain.MO.NET>, akravetz at Walden.MO.NET says:
>What causes a gel to smile, meaning the bands to curve upward and out?? I 
>run a lot of minigels and sometimes get that effect on both the edges and 
>the middle of the gel. Real pain in the neck. Any help would be 
>appreciated. I use 1xTAE gels (1 percent)
>
>thanks
>
>andy
>

Andy:

What do you mean by smiling ? there are two types of smiling:

1. Gel smiling: The bands of the middle lanes run faster than 
those at the edge of the gel (typical for sequencing gels) 
This phenomenon is due to temperature differences (middle vs border) 
in the gel which cause different resistance. 
It can be avoided by running the gel slowlier and by preruning the 
gel to heat it up regularly.

2. Band smiling: [((((] the band curve upwards at both ends.
 This is most likely caused by overloading and running in prestained 
gels i.e. when you put EtBr into the gel prior to casting. 
The DNA takes up EtBr while migrating, leaving a trace containing 
less EtBr. That's why upper bands are often weaker (less EtBr 
available). But the band also looses material, causing an usually
 non-visible smear behind it in EtBr-containg gels. 
(This smear is well visible in SybrGreen, post-runing stainings).
 If the gel is prestained with EtBr,  the dye will diffuse  from 
the sides (where it is present at higher concentration) into the 
trace with less EtBr and will partially, i.e. at the sides of the
 lane make the DNA-smear visible, leading to the upward bending of 
the band.
This can be avoided by pouring the gel w/o EtBr and staining the
 gel AFTER runing. But the disadvantage is that then you often 
might see the whole semar behind the band.


Sui



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