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My question maybe very primary, but after I learned this part, questions always follow me. SDS-PAGE gel works for detect protein, agarose gel works for detect nucleic acid, so here is my question: 1. Why does SDS-PAGE works for protein, and agarose gel works for nucleic acid? Is it any possible to use SDS-PAGE to detect DNA? Or use agarose to detect protein?

  1. Why does the SDS-PAGE gel always runs vertically, and agarose gel runs horizontally? Are they necessary?

  2. Is any other material could be use in gel electrophoresis?

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  • $\begingroup$ Mad Scientist explains why you would make different choices regarding size and desired resolution. Polyacrylamide gels can provide a higher degree of resolution for small molecules, you need to realize that proteins are small. A good-sized protein is around 400kDa., where as a 1000bp DNA molecule is 650kDa. Agarose pore structure is larger, so you use it for larger molecules like DNA. Another reason is toxicity. Polyacrylamide is a toxic substance, Agarose is a sugar, so if you can avoid using polyacrylamide, you do; sometimes you can't. $\endgroup$
    – AMR
    Commented Oct 4, 2015 at 4:37

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You can use polyacrylamide gels for RNA and DNA, and this is the common way to examine shorter nucleic acids. Agarose gels can be used for larger nucleic acids like plasmids that are a few thousand base pairs long, polyacrylamide gels work better for shorter nucleic acids around a hundred nucleotides long.

You don't need SDS for nucleic acids, they already have a negative charge at the phosphate backbone. Polyacrylamide gels for nucleic acids also don't use a separate stacking gel like in SDS-PAGE, it is just one single gel.

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  • $\begingroup$ You just answered the first question, it makes sense to me, thank you. But could please answer the 2nd and 3rd questions? $\endgroup$
    – sunboyharry
    Commented Oct 16, 2015 at 1:25

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