Smiling of bands near the edges of DGGE gels appears to be endemic in all systems. What is the exact cause of this?
We had the same problem in our lab. In our case the Ammonium per sulfate we used was prepared long time ago and we concluded that it expired or evaporated, thus it was not the concentration it was needed to be. I suggest you should make all your solutions again from scratch.
Be sure your buffers are fresh. We hand-make our gels, using fresh APS every time and pre-made acrylamide. We only get smiling (or frowning) gels when we dont load even volumes into all of the wells. If we dont load any protein sample into the wells, we use the same volume of cell lysis buffer (RIPA in our case) as the other samples (to make all the wells equal in volume). We then add the same amount of SLB to every well...even to the wells that have the ladder. When we do this, we can run the gel at 120V at RT and get a gel that runs VERY straight. People usually see the "smile" because they don't add anything, or add less volume, to the outside wells.
Check gel wells for bubbles. If they are present allow longer polymerization of in-house made gels or add more APS and TEMED (easily can triple the amount).
As already said before, the distribution of the gel components and the heat distribution are the key elements here. When casting your gradient gel, make sure the components are evenly distributed (not only cast from the middle but move the needle or whatever you use for filling the gel in the glass slide from side to side while casting the gel). Otherwise you will get an uneven gradient that causes smiling.
Leakage, so never use the last well at both ends. It is best to balance the loading & leave the last 2 wells at the two end vacant
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