화학공학소재연구정보센터
Electrophoresis, Vol.31, No.20, 3446-3449, 2010
Physical interpretation of the L-r parameter in the theory for the gel electrophoresis of partially denatured DNA
Partial strand melting of dsDNA during gel electrophoresis typically results in an abrupt reduction of mobility. Several DNA analysis technologies are based on this phenomenon. Inspired by the de Gennes' theory for the reptation of branched polymers in gels, Lerman et al. (Ann. Rev. Biophys. Bioeng. 1984, 13, 399-423) proposed a mathematical expression to predict this reduced mobility. The latter contains only two parameters: the average number of denatured bases (p) over bar p (which can be obtained using a theory for DNA melting) and a constant L-r. However, there is confusion in the literature regarding the physical interpretation of L-r and little is known about its dependence upon experimental parameters. The purpose of this short communication is to derive an explicit equation for the parameter L-r from the de Gennes theory of reptation. Our derivation shines light on the meaning of L-r, clarifies the scope of the underlying approximations, and makes predictions about the dependence of L-r upon the gel pore size and the persistence length of ssDNA.