14 research outputs found
Hybridization Thermodynamics of DNA Oligonucleotides during Microchip Capillary Electrophoresis
Capillary
electrophoresis (CE) is a powerful analytical tool for performing
separations and characterizing properties of charged species. For
reacting species during a CE separation, local concentrations change
leading to nonequilibrium conditions. Interpreting experimental data
with such nonequilibrium reactive species is nontrivial due to the
large number of variables involved in the system. In this work we
develop a COMSOL multiphysics-based numerical model to simulate the
electrokinetic mass transport of short interacting ssDNAs in microchip
capillary electrophoresis. We probe the importance of the dissociation
constant, <i>K</i><sub>D</sub>, and the concentration of
DNA on the resulting observed mobility of the dsDNA peak, ÎĽ<sub>w</sub>, by using a full sweep of parametric simulations. We find
that the observed mobility is strongly dependent on the DNA concentration
and <i>K</i><sub>D</sub>, as well as ssDNA concentration,
and develop a relation with which to understand this dependence. Furthermore,
we present experimental microchip capillary electrophoresis measurements
of interacting 10 base ssDNA and its complement with changes in buffer
ionic strength, DNA concentration, and DNA sequence to vary the system
equilibria. We then compare our results to thermodynamically calculated <i>K</i><sub>D</sub> values