Electrokinetic separation of DNA oligomers is a fundamental procedure in bioanalytical chemistry. While length resolution is typically achieved by the use of polymer gels as sieving matrices, a faster alternative is to end-label oligomers with uncharged objects so that the charge-to-mass ratio varies with oligomer length. With this goal in mind, we have been exploring the use of nonionic micelles as end-labels for DNA in capillary electophoresis. DNA oligomers of interest are end-alkylated (either covalently or by hybridization of an alkylated probe) to provide for interaction with micelles. Unlike covalently attached polymers or proteins, nonionic micelles transiently attach to alkylated DNA by a co-assembly mechanism, and this provides important advantages in bioanalytical applications. One is that the mobility of the alkylated DNA can be tuned to prevent co-migration of oligomers. Using open-channel capillary electrophoresis in the presence of Triton X-100, we demonstrate that DNA mobility is a very strong function of the attached alkane length in the range of C12 to C18. A phase partitioning model is presented that fully accounts for the effect of alkane length, DNA oligomer length, micelle size, and micelle concentration on the observed mobility. The model can be used to measure the length of alkylated DNA, and model parameters can be predicted by thermodynamics of the co-assembly process. Bi-alkylated DNA oligomers have also been synthesized. The combined effect of micelles at each end on is found to be additive for long oligomers, but is attenuated for short ones due to hydrodynamic communication between the micelles.