Separations of DNA fragments by capillary electrophoresis in N-substituted polyacrylamides

Abstract

In spite of its high resolving capability, the use of polyacrylamide as a sieving matrix for capillary electrophoresis (CE) is limited by several factors. The viscosity of polyacrylamide solutions is too high for easy capillary filling and the matrix requires a highly pressurized system to be replaced after each run. The systems currently used to produce short polyacrylamide chains needed to overcome this problem, require a careful optimization of polymerization conditions to produce polymers of reproducible composition. In addition, the polyacrylamide viscosity may vary with time depending on the shear stress to which the solution is subjected. This work proposes some new matrices for DNA separations by CE that overcome these obstacles while maintaining the high resolution offered by polyacrylamide. The properties of dimethylacrylamide and poly(acryloylaminoethoxy)ethyl-β- d-glucopyranoside were investigated. Both polymers were found to be more suitable than polyacrylamide as DNA sieving media. The presence of substituents on the amido nitrogen reduces the viscosity of the polymer solutions without changing separation selectivity as demonstrated by the identical profile of the double-log curves of mobility versus DNA size obtained for the three polymers. In general, an increase in the monomer size leads to the formation of a network with larger pore sizes in which DNA molecules migrate more rapidly, providing shorter analysis times and more efficient separation.