Less-than-optimal transfer in the second gel is not uncommon and frequently requires adjustments in protocol. To achieve similar transfer efficiencies in the two gels you can transfer them one at a time or consider the following suggestions:
Make sure that the blot module is not overfilled with buffer, i.e., fill to point where pads are just covered and no higher. If the buffer level is too high, some current will bypass the gels. If it is overfilled, shorting, arcing, and other problems can occur.
Use antioxidant when transferring reduced proteins.
Increase transfer time by 30 to 60 minutes. The longer run time allows the slower moving proteins time to move out of the gel.
As proteins are being driven out of the gel by the SDS on their surface, it is important that enough is retained to keep them mobile. However, the methanol that is included in the transfer buffer will remove some of the SDS, and the higher the methanol concentration, the more SDS is washed off of the protein. Methanol is included in order to increase binding to nitrocellulose membranes via hydrophobic interactions. However, if using PVDF or nylon membranes, less or even no methanol may be required. 20% methanol is a good starting point for most situations In the event that the transfer is less than ideal, methanol levels should be reduced by at least 50%. The optimal percentage should be determined empirically. Something to keep in mind is that with increased mobility, the proteins may just move straight though the first membrane. In this case, a second membrane may trap these samples.
It is possible to BRIEFLY (1 min) soak the second gel in transfer buffer with 0.01 to 0.02% SDS before assembling the sandwich. This must be a short soak or the proteins will tend to diffuse out of the gel.
Adding 0.01-0.02% SDS to the transfer buffer and using it for the transfer will also aid in protein mobility.
Halfway through the transfer process (30 min), swap the front gel and back gel in the blotter. This is fairly easy to do if you just swap pad-paper-gel-membrane-pad sections.
Another recommendation: if you must transfer simultaneously, and want to be able to compare results of both blots, use an internal control in both gels to get an idea of the relative transfer efficiency and to afford some normalization of the results.
Find additional tips, troubleshooting help, and resources within our
Protein Electrophoresis and Western Blotting Support Center.