The Role of Topology in DNA Gel Electrophoresis

Abstract

Topology plays a key role in the biophysics of DNA, and is intimately related to its functioning. For instance, transcription of a gene redistributes twist locally to create what is known as supercoiling, while catenanes or knots can prevent cell division, hence they need to be quickly and accurately removed by specialised enzymes known as topoisomerases. But how can one establish experimentally the topological state of a given DNA molecule? By far the most successful and widely used technique for this is gel electrophoresis (Calladine et al. 1997; Bates and Maxwell 2005). This method exploits the empirical observation that the mobility of a charged DNA molecule under an electric field and moving through a gel depends on its size, shape and topology (Bates and Maxwell 2005; Stasiak et al. 1996). Nowadays, gel electrophoresis is a ubiquitous technique (Calladine et al. 1997; Viovy 2000; Dorfman 2010), since it readily allows the separation of polymers with different physical properties and it is systematically used for DNA identification and purification (Calladine et al. 1997).