page_title: Gel electrophoresis
section_title: Denaturing
hierarchical_section_title: Gel electrophoresis / Gel conditions / Denaturing
caption_attribution_description: English: TGE profiles representing the bifidobacterial diversity of fecal samples from two healthy volunteers (A and B) before and after AMC exposure. 1:day-12; 2:day-6; 3:day 0; 4:day 5; 5:day 8; 6:day 12; 7:day 19; 8:day 26; 9:day 33; 10:day 64. a, b, d, e, f, a′: B. adolescentis; c, g: B. bifidum; b′: B. pseudocatenulatum; c′: B. longum; d′: B. dentium; e′: B. breve; f′: B. pseudolongum; g′: B. animalis subsp. lactis. doi:10.1371/journal.pone.0050257.g004
context_page_description: Gel electrophoresis is a method for separation and analysis of macromolecules and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.
  Nucleic acid molecules are separated by applying an electric current to move the negatively charged molecules through a matrix of agarose or other substances. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel. This phenomenon is called sieving. Proteins are separated by the charge in agarose because the pores of the gel are too small to sieve proteins. Gel electrophoresis can also be used for the separation of nanoparticles.
  Gel electrophoresis uses a gel as an anticonvective medium or sieving medium during electrophoresis, the movement of a charged particle in an electrical current.
context_section_description: 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).
caption: TTGE profiles representing the bifidobacterial diversity of fecal samples from two healthy volunteers (A and B) before and after AMC (Oral Amoxicillin-Clavulanic Acid) treatment
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