page_title: Gel electrophoresis of nucleic acids
section_title: Size of DNA
hierarchical_section_title: Gel electrophoresis of nucleic acids / Factors affecting migration of nucleic acids / Size of DNA
caption_attribution_description: Plasmid miniprep. 0.8% agarose gel, ethidium bromide-stained.
context_page_description: Nucleic acid electrophoresis is an analytical technique used to separate DNA or RNA fragments by size and reactivity. Nucleic acid molecules which are to be analyzed are set upon a viscous medium, the gel, where an electric field induces the nucleic acids to migrate toward the anode. The separation of these fragments is accomplished by exploiting the mobilities with which different sized molecules are able to pass through the gel. Longer molecules migrate more slowly because they experience more resistance within the gel. Because the size of the molecule affects its mobility, smaller fragments end up nearer to the anode than longer ones in a given period. After some time, the voltage is removed and the fragmentation gradient is analyzed. For larger separations between similar sized fragments, either the voltage or run time can be increased. Extended runs across a low voltage gel yield the most accurate resolution. Voltage is, however, not the sole factor in determining electrophoresis of nucleic acids.
  The nucleic acid to be separated can be prepared in several ways before separation by electrophoresis.
context_section_description: The gel sieves the DNA by the size of the DNA molecule whereby smaller molecules travel faster. Double-stranded DNA moves at a rate that is approximately inversely proportional to the logarithm of the number of base pairs.  This relationship however breaks down with very large DNA fragments and it is not possible to separate them using standard agarose gel electrophoresis.  The limit of resolution depends on gel composition and field strength. and the mobility of larger circular DNA may be more strongly affected than linear DNA by the pore size of the gel.  Separation of very large DNA fragments requires pulse field gel electrophoresis (PFGE).  In field inversion gel electrophoresis (FIGE, a kind of PFGE), it is possible to have "band inversion" - where large molecules may move faster than small molecules.
caption: Gels of plasmid preparations usually show a major band of supercoiled DNA with other fainter bands in the same lane.  Note that by convention DNA gel is displayed with smaller DNA fragments near the bottom of the gel.  This is because historically DNA gel were run vertically and the smaller DNA fragments move downwards faster.
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