Hi there,

First impression : it looks overloaded. Second impression: the front of bands is not regular which might account for a perturbed interface between separating and stacking gels (did you cover gel surface with water or isopropanol during lower gel polymerization?). Sample high salt composition might also interfere with the running.

You seem to have 2 issues, so if you could answer a few questions. Were these gels purchased or did you make them? Were all of the lane samples in similar preparations (ie. in the same chemicals?) Did you overrun your gel as I don't see your sample buffer front at the bottom?

Common issues that cause what your seeing: 1)The gels or buffers were made improperly (ie bad gradients, wrong salt, wrong buffering system) , 2) The gels went bad (ie expired, gels got hot and melted) 3) The charge was incorrect (ie too much amperage) 3) There was an incompatible chemical in your sample buffer, or running buffer, 4) your samples were overloaded 5) your protein started precipitating during the run.

If the gels were purchased, then I would guess something in the actual samples. Also, lanes 3,5,6,7, and 8 were overloaded.  If you could answer the above, I could judge better, but my initial observations are lanes 1,4 and 6 have a chemical which is causing one issue and overloading 3,5,6,7 and 8 are causing a second problem.  

Liger,

Hearty thank you for your significant suggestion. I loaded just 10ul, In the beginning of the run the bands look fine but become fat as goes down. Yes I did cover surface of the gel before I put stacking gel. Those bands which are coming to move slower are the membrane proteins reconstituted in micelles that could be the reason they are behaving different than the other samples.  

Adam,

I really appreciate your suggestions.  I prepared the gel myself using biorad recipe. The acylamide was purchased last year. No they are in different chemicals. No I didn't overrun it. This is the picture during the running time not the gel after staining and destaining. I am eager to have more suggestions.

Based on the assumption that the gel was made properly?, the buffers are correct? and The charge was correct? Also based on your above statement about the sample containing micelles, I would guess that it was your micelles is causing the irregularities in lanes 1,4 and 6. It would explain why the bands look like tree branches, which would be caused by different sized micelles, getting stuck at different places in the gel. I don't know what your compound is made of, so I cant help you with that, but you need to break the micelles up prior to gel loading and prevent them from aggregating during/prior to the run.  In lanes 3,5,6,7 and 8 you need to dilute your samples 1:5-1:10

Were you able to fix this problem? If so, what was the solution in your case?

 Hi Merdzo,

With the lots of good suggestions I was able to troubleshoot this problem. Actually my sample buffer was bad. I just tried different recipe for sample buffer online and it worked well.