Cracking buffer principles
Cracking buffer principles

Samples are applied to SDS gels in "cracking" buffer. The term "cracking" comes from the fact that cells are often disrupted directly in the buffer

I'm skeptical of recipes and prefer principles.

For any procedure, begin with a recipe. Typically I take a literature recipe. I then examine each component of the recipe. If a component is obviously superfluous, I leave it out. If it's obviously suboptimal I adust it. Ultimately I may systematically vary critical variables to optimize. If I overlook a critical variable I'll wind up with a poor procedure. This is why it's helpful to discuss procedures with knowledgeable people. The beginner may ask "How should I know what the components do?" If you're not curious enough to find out, reconsider becoming a scientist. Paying attention pays dividends, sometimes in unexpected ways, in the long run.

I've used a variety of "cracking" buffers. Generally I have a 10X stock of high pH (~8.5 or higher, ~0.5M) tris buffer (i.e. 0.5M tris, 0.1M MOPS), a 0.5M DTT solution (~100X, must be fresh), a 10%w/v SDS solution (~10X), a dye stock solution (~1% crystal violet) and something to make the sample dense (sucrose or preferably Ficoll). Components, particularly SDS and DTT can be varied systematically to assure that concentrations are sufficient. One can easily make and test a variety of 10X buffer solutions.

Buffer - Should be high pH to facilitate reduction (but avoid alkaline hydrolysis). If you're applying a large volume conductivity (buffer concentration) shouldn't be too high. Acid containing samples may raise buffering requirements. Borate is useful where reactive amines are problematic (borax is a primary buffer standard)

Reducing agent - if you're going to alkylate you need a low concentration of a strong reductant. Ambient oxygen oxidizes thiols so pay attention to the quality of the reductant (for DTT see)

SDS - 0.1% will do for small amounts of protein, but be aware that lipids, nonionic detergents, excessive protein, etc. can raise the requirement dramatically.

Dye - Crystal violet (cation) binds SDS and runs toward the cathode. It lets you see the sample and track migration. If your sample contains acid you may prefer an indicator dye that tells you if your buffer has failed to neutralize the acid.

Ficoll - Ficoll is a roughly spherical polymer. In increases density but keeps viscosity and osmolarity low.