Editing Agarose gel electrophoresis (section)

===Electrophoresis===
[[File:Electrophoresis - Moving along gel.jpg|thumb|Agarose gel slab in electrophoresis tank with bands of dyes indicating progress of the electrophoresis. The DNA moves towards anode.]]
Agarose gel electrophoresis is most commonly done horizontally in a subaquaeous mode whereby the slab gel is completely submerged in buffer during electrophoresis. It is also possible, but less common, to perform the electrophoresis vertically, as well as horizontally with the gel raised on agarose legs using an appropriate apparatus.<ref>{{cite book |title=Physical Biochemistry: Applications to Biochemistry and Molecular Biology |author =David Freifelder |edition=2nd |year=1982 |publisher=WH Freeman |pages= 292–293 |isbn= 978-0716714446}}</ref>  The buffer used in the gel is the same as the running buffer in the electrophoresis tank, which is why electrophoresis in the subaquaeous mode is possible with agarose gel.

For optimal resolution of DNA greater than 2{{Spaces}}kb in size in standard gel electrophoresis, 5 to 8 V/cm is recommended (the distance in cm refers to the distance between electrodes, therefore this recommended voltage would be 5 to 8 multiplied by the distance between the electrodes in cm).<ref name=sambrook1/>   Voltage may also be limited by the fact that it heats the gel and may cause the gel to melt if it is run at high voltage for a prolonged period, especially if the gel used is LMP agarose gel. Too high a voltage may also reduce resolution, as well as causing band streaking for large DNA molecules. Too low a voltage may lead to broadening of band for small DNA fragments due to dispersion and diffusion.<ref>{{cite web |url=http://bio.lonza.com/uploads/tx_mwaxmarketingmaterial/Lonza_BenchGuides_SourceBook_Section_III_-_Loading_and_Running_DNA_in_Agarose_Gels.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://bio.lonza.com/uploads/tx_mwaxmarketingmaterial/Lonza_BenchGuides_SourceBook_Section_III_-_Loading_and_Running_DNA_in_Agarose_Gels.pdf |archive-date=2022-10-09 |url-status=live |title=Section III: Loading and Running DNA in Agarose Gels |work=Lonza Group }}</ref>

Since DNA is not visible in natural light, the progress of the electrophoresis is monitored using colored dyes. Xylene cyanol (light blue color) comigrates large DNA fragments, while Bromophenol blue (dark blue) comigrates with the smaller fragments. Less commonly used dyes include [[Cresol Red]] and [[Orange G]] which migrate ahead of bromophenol blue. A [[Molecular weight size marker|DNA marker]] is also run together for the estimation of the molecular weight of the DNA fragments. Note however that the size of a circular DNA like plasmids cannot be accurately gauged using standard markers unless it has been linearized by [[restriction digest]], alternatively a supercoiled DNA marker may be used.