Separation of RNA and DNA in Methylmercuric Hydroxide Denaturing Agarose Gels


RNA molecules tend to aggregate in solution and adopt a range of conformations that can affect the mobility of molecules. In addition, nuclease nicks are often not revealed by nondenaturing electrophoresis. For this reason, it is often preferable to separate nucleic acids as denatured molecules. The use of gels containing millimolar amounts of methylmercuric (II) hydroxide as the denaturing agent is described. Heating and other operations must be carried out in an efficient fume hood because methylmercury (II) hydroxide is extremely poisonous, and it should be used and disposed of in accordance with the supplier's instructions.

Keywords: RNA; DNA; denaturation; methylmercuric hydroxide

Figure 1.

Submarine slab gel apparatus.



Bailey JM and Davidson N (1976) Methylmercury as a reversible denaturing agent for agarose gel electrophoresis. Analytical Biochemistry 70: 75.

Fangman WL (1978) Separation of very large DNA molecules by gel electrophoresis. Nucleic Acids Research 5: 53–65.

Further Reading

Jovin TM (1971) Electrophoretic fractionation of oligodeoxyribonucleotides. Methods in Enzymology 21: 179.

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Southern, Edwin M(Jul 2003) Separation of RNA and DNA in Methylmercuric Hydroxide Denaturing Agarose Gels. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0003781]