Denaturing gels are run under conditions that disrupt the natural structure of the analyte, causing it to unfold into a linear chain.  Thus, the mobility of each macromolecule depends only on its linear length and its mass-to-charge ratio.  Thus, the secondary, tertiary, and quaternary levels of biomolecular structure are disrupted, leaving only the primary structure to be analyzed.
Nucleic acids are often denatured by including urea in the buffer, while proteins are denatured using sodium dodecyl sulfate, usually as part of the SDS-PAGE process.  For full denaturation of proteins, it is also necessary to reduce the covalent disulfide bonds that stabilize their tertiary and quaternary structure, a method called reducing PAGE. Reducing conditions are usually maintained by the addition of beta-mercaptoethanol or dithiothreitol. For a general analysis of protein samples, reducing PAGE is the most common form of protein electrophoresis.
Denaturing conditions are necessary for proper estimation of molecular weight of RNA. RNA is able to form more intramolecular interactions than DNA which may result in change of its electrophoretic mobility. Urea, DMSO and glyoxal are the most often used denaturing agents to disrupt RNA structure. Originally, highly toxic methylmercury hydroxide was often used in denaturing RNA electrophoresis, but it may be method of choice for some samples.
Denaturing gel electrophoresis is used in the DNA and RNA banding pattern-based methods temperature gradient gel electrophoresis (TGGE) and denaturing gradient gel electrophoresis (DGGE).