Gel Smiling

[Andy Kravetz]

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

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"I love the wild power of language and and the purity of the madness that
governs it and makes it music"
-HST, _Generation of Swine_
Andy Kravetz
Freelance Journalist
St. Louis, Missouri
akra...@walden.mo.net
http://walden.mo.net/~akravetz/

[Sarah Tamara Braun]

In Article <44g2b7$6...@Twain.MO.NET>, akra...@Walden.MO.NET (Andy Kravetz)
wrote:

>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
>

Possibly, you are running your gels at too high a voltage.
Voltage should be below 110 V for a 1% TAE gel.

Also, running near the edges can cause that, so maybe not
using the furthest lanes.

Cheers,

Sarah Tamara Braun

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[Sui Huang]

In article <44g2b7$6...@Twain.MO.NET>, akra...@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

[Duncan Clark]

If the electrodes are close to the gel and do not go all the way across
the gel apparatus then that can lead to a field distortion at the edges
hence a smile.

Duncan
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My mind's made up. Don't confuse me with the facts!