Theory of band broadening for DNA gel electrophoresis and sequencing

Abstract

The problem of (thermal) band broadening during DNA gel electrophoresis is studied analytically and numerically using the reptation model. It is shown that the orientation of the end-to-end vector of the molecules leads to increased diffusion and even to molecular size-independent band broadening. Thus, the Einstein relation between mobility and diffusion holds for only very small molecules. Also, "self-trapped" molecules are predicted to give fuzzy bands, as observed experimentally. Finally, megabase molecules are discussed and the consequences of our predictions for the improvement of sequencing are considered.