Using copper plates to distribute heat evenly across the gel



Below are some pictures comparing the running of a gel under several conditions.  It is important while running a gel to ensure that heat is evenly distributed across the entire gel.  This keeps everything moving through the gel at the same realtive speed.

While running, a gel normally becomes warmer in the middle than at its outside edges.  This leads to faster movement through the middle of the gel than at the outside edges.  A "smiling" effect results.  (See here for an example of "smiling.")

In order to spread the heat produced during the run of the gel evenly, some copper plates were obtained and used.  They were clamped to the glass plates containing the gel.  (Pictures the apparatus will arrive in due time . . .)   They appear to work quite well.
 


Above are two pictures of the same gel.  (Actually, three pictures of the gel, since the first image here is a combination of two pictures that were taken.  The 32 cm long gel is too large to view all at one time on the transilluminator being used to take the pictures.)  This 15% gel was run at 6 W for 32 hours.  As can be seen, it could have run for quite a while longer without the samples running off the end of the gel.

A slight "smiling" effect can be seen as well.  Specifically, notice the lanes that contain samples of a known 25bp ladder.  (This molecular marker has fragments ranging from 25 to 300 base pairs [bp] long in steps of 25.)  Notice that the two lanes (far right and 5th from the right) that contain the 25bp ladder samples do not have bands in exactly the same locations.  No copper plates were used on this gel.
 


The two pictures above are from the first gel run with the copper plates.  It was a 15% gel run at 6 W for 34 hours.  It cannot be seen in these pictures, but the samples ran about the same distance as (only slightly farther than) the previous gel.  This gel ran evenly across its entire width.  Notice again the lanes that contain the 25bp ladder (on the first of the 2 pictures, the far right and the 5th from the right lanes).  The bands in these lanes are at the same locations.  This precision is necessary when the exact length of the unknown sample bands must be determined.

The tables along the side of (or on top of . . .) the gel indicate the calculated length of the unknown bands of DNA.  For example, the band labeled "14" in the lane second from the left has been calculated as being 272bp (base pairs: A, T, G, C) in length.  Similarly, bands 6 and 7 have been calculated as having 278bp and 272bp respectively.

The following diagram is another representation of the data. . . .
 

Here is shown the same data as above in graphical form.  The peaks indicate where the bands occur.  Lanes 8 and 12 contain the data from the 25bp ladders (each having three peaks clearly visible) and lane 1 contains the data from the 1Kb ladder.  The other lanes (2-7, 9-11) contain the data from the iguana DNA that has been amplified with site specific primers in the PCR process.  As hoped, wished, and desired, each has only either one or two peaks (. . . strong peaks anyway).  (See the page about microsatellites for an explanation of why.)
 

Currently, a gel is running at 12 W and appears to be running evenly.  Next comes 24 W.  :)
 
 

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