Editing Agarose gel electrophoresis (section)

===Mechanism of migration and separation===

The negative charge of its phosphate backbone moves the DNA towards the positively charged anode during electrophoresis. However, the migration of DNA molecules in solution, in the absence of a gel matrix, is independent of molecular weight during electrophoresis.<ref name="zimm"/><ref name="old & primrose">{{cite book |title=Principle of Gene Manipulation - An Introduction to Genetic Engineering |author1=Robert W. Old |author2=Sandy B. Primrose |page=[https://archive.org/details/principlesofgene00oldr/page/9 9] |publisher=Blackwell Scientific |edition=5th |isbn=9780632037124 |url=https://archive.org/details/principlesofgene00oldr/page/9 |date=1994-09-27 }}</ref>  The gel matrix is therefore responsible for the separation of DNA by size during electrophoresis, and a number of models exist to explain the mechanism of separation of biomolecules in gel matrix. A widely accepted one is the Ogston model which treats the polymer matrix as a sieve. A globular protein or a [[random coil]] DNA moves through the interconnected pores, and the movement of larger molecules is more likely to be impeded and slowed down by collisions with the gel matrix, and the molecules of different sizes can therefore be separated in this sieving process.<ref name="zimm" />

The Ogston model however breaks down for large molecules whereby the pores are significantly smaller than size of the molecule. For DNA molecules of size greater than 1 kb, a [[reptation]] model (or its variants) is most commonly used. This model assumes that the DNA can crawl in a "snake-like" fashion (hence "reptation") through the pores as an elongated molecule. A biased reptation model applies at higher electric field strength, whereby the leading end of the molecule become strongly biased in the forward direction and pulls the rest of the molecule along.<ref name="microfluidics">{{cite book |chapter-url=https://books.google.com/books?id=8wyBp-vKbdcC&pg=PA125 |title=Microfluidics for Biological Applications |editor1=Tian, Wei-Cheng |editor2=Finehout, Erin |chapter=Chapter 4 - Genetic Analysis in Miniaturized Electrophoresis Systems |author1=Li Zhu |author2=Hong Wang |page=125 |publisher=Springer |isbn=978-0-387-09480-9 |date=2009-03-02 }}</ref>  Real-time fluorescence microscopy of stained molecules, however, showed more subtle dynamics during electrophoresis, with the DNA showing considerable elasticity as it alternately stretching in the direction of the applied field and then contracting into a ball, or becoming hooked into a U-shape when it gets caught on the polymer fibres.<ref>{{cite journal | vauthors = Smith SB, Aldridge PK, Callis JB | title = Observation of individual DNA molecules undergoing gel electrophoresis | journal = Science | volume = 243 | issue = 4888 | pages = 203–6 | date = January 1989 | pmid = 2911733 | doi = 10.1126/science.2911733 | bibcode = 1989Sci...243..203S }}</ref><ref>{{cite journal | vauthors = Schwartz DC, Koval M | title = Conformational dynamics of individual DNA molecules during gel electrophoresis | journal = Nature | volume = 338 | issue = 6215 | pages = 520–2 | date = April 1989 | pmid = 2927511 | doi = 10.1038/338520a0 | bibcode = 1989Natur.338..520S | s2cid = 4249063 }}</ref>