Branched polymeric labels used as drag-tags in free-solution electrophoresis of ssDNA

Abstract

In the framework of the classical blob theory of end-labeled free-solution electrophoresis of ssDNA, and based on recent experimental data with linear and branched polymeric labels (or drag-tags), the present study puts forward design principles for the optimal type of branching that would give, for a given total number of monomers, the highest effective frictional drag for ssDNA sequencing purposes. The hydrodynamic radii of the linear and branched labels are calculated using standard models like the freely jointed chain model and the Kratky-Porod worm-like chain model. Based on comparisons of the theory with the experimental data, we propose that the design of new branched labels should use either side chains whose length is comparable to the distance between the branching points or two long branches located near the ends of the molecule's backbone.