Electric field mediated DNA motion model

Understanding the motion and the governing equations of a molecule's path in tissue is an ultimate requirement for the repeatable, site specific delivery of molecules [Joseph D. Hickey. Modelling the Motion of Ions and Molecules in Electroporation and Electrophoresis Field Conditions. University of South Florida, College of Arts and Sciences, Department of Physics, Tampa, Florida, 2003., Joseph D. Hickey and Richard Gilbert. Modeling the electromobility of ions in a target tissue. DNA and Cell Biology, 22 (12) (2003) 823-828.]. This paper describes a computationally efficient mathematical model and simulation technique for the examination of DNA fragments in a 1% agarose gel. The speed of the individual DNA fragments through the agarose gel was described through two parts. The maximum velocity was calculated using the Coulombic force divided by Stoke's law and that value was retarded by an exponential rate equation. The simulation utilizes previously published techniques modified for this specific application [Joseph D. Hickey and Richard Gilbert. Fluid flow electrophoresis model. Bioelectrochemistry, 63 (2) (2004) 365-367., Joseph D. Hickey and Richard Gilbert. Modeling the electromobility of ions in a target tissue. DNA and Cell Biology, 22 (12) (2003) 823-828.]. Five representative DNA fragment sizes that span the resolution of a 1% agarose gel were chosen for this analysis. The speeds corresponding to these five DNA fragment sizes were converted into discrete values and used in a 50 step simulation. The resultant error comparing the simulation with experimental distance was 7.76%. Through a 1-D optimization procedure, this error was reduced to 3.02% for a 52 step simulation.