Editing Gel electrophoresis (section)

===Denaturing===
[[File: TTGE profiles representing the bifidobacterial diversity of fecal samples journal pone 0050257 g004.png|thumb|400px|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]]

[[Denaturation (biochemistry)|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 [[Polyacrylamide gel electrophoresis|SDS-PAGE]] process.  For full denaturation of proteins, it is also necessary to reduce the covalent [[disulfide bond]]s that stabilize their [[tertiary structure|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]], [[Dimethyl sulfoxide|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,<ref name="pmid632280">{{cite journal| author1=Buell GN| author2=Wickens MP| author3=Payvar F| author4=Schimke RT| title=Synthesis of full length cDNAs from four partially purified oviduct mRNAs. | journal=J Biol Chem | year= 1978 | volume= 253 | issue= 7 | pages= 2471–82 | pmid=632280 | doi= 10.1016/S0021-9258(17)38097-3| pmc= | doi-access=free }}</ref> but it may be method of choice for some samples.<ref name="pmid2570517">{{cite journal | author= Schelp C, Kaaden OR | title= Enhanced full-length transcription of Sindbis virus RNA by effective denaturation with methylmercury hydroxide. | journal= Acta Virol | year= 1989 | volume= 33 | issue= 3 | pages= 297–302 | pmid= 2570517 | doi=  | pmc=  | url= https://pubmed.ncbi.nlm.nih.gov/2570517 | access-date= 23 March 2022 | archive-date= 11 June 2022 | archive-url= https://web.archive.org/web/20220611043435/https://pubmed.ncbi.nlm.nih.gov/?Db=pubmed&Cmd=Retrieve&dopt=abstractplus&list_uids=2570517 | url-status= live }}</ref>

Denaturing gel electrophoresis is used in the DNA and RNA banding pattern-based methods [[temperature gradient gel electrophoresis]] (TGGE)<ref name="pmid12460271">{{cite journal| author1=Fromin N| author2=Hamelin J| author3=Tarnawski S| author4=Roesti D| author5=Jourdain-Miserez K| author6=Forestier N| display-authors=etal| title=Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns.| journal=Environ Microbiol| year=2002| volume=4| issue=11| pages=634–43| pmid=12460271| doi=10.1046/j.1462-2920.2002.00358.x| pmc=| bibcode=2002EnvMi...4..634F| url=https://pubmed.ncbi.nlm.nih.gov/12460271| access-date=23 March 2022| archive-date=11 June 2022| archive-url=https://web.archive.org/web/20220611043437/https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1046/j.1462-2920.2002.00358.x?sid=nlm%3Apubmed| url-status=live}}</ref> and denaturing gradient gel electrophoresis (DGGE).<ref name="pmid369706">{{cite journal | author1=Fischer SG | author2=Lerman LS | title=Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. | journal=Cell | year=1979 | volume=16 | issue=1 | pages=191–200 | pmid=369706 | doi=10.1016/0092-8674(79)90200-9 | pmc= | s2cid=9369012 | url=https://pubmed.ncbi.nlm.nih.gov/369706 | access-date=23 March 2022 | archive-date=11 June 2022 | archive-url=https://web.archive.org/web/20220611043438/https://www.cell.com/cell/pdf/0092-8674(79)90200-9.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2F0092867479902009%3Fshowall%3Dtrue | url-status=live }}</ref>