Adverse-Mode FFF: Multi-Force Ideal Retention Theory

A novel field-flow fractionation (FFF) technique, in which two opposing external forces act on the solute particles, is proposed. When the two external forces are sufficiently strong and scale differently as a function of the solutes’ property of interest (such as the solute particle size), a sharp peak in the retention ratio (dramatic drop in elution time) is predicted to exist. Because the external forces oppose one another, we refer to this novel technique as adverse-mode FFF. The location of this peak is theoretically predicted and its ideal width estimated. The peak can become quite sharp by simultaneously increasing the strength of both fields, suggesting that adverse-mode FFF could be a useful technique for accurately measuring single species solute size

Solid Phase DNA Amplification: A Brownian Dynamics Study of Crowding Effects

AbstractSolid phase amplification (SPA), a new method to amplify DNA, is characterized by the use of surface-bound primers. This limits the amplification to two-dimensional surfaces and therefore allows the easy parallelization of DNA amplification in a single system. SPA leads to the formation of small but dense DNA brushes, called DNA colonies. For a molecule to successfully duplicate itself, it needs to bend so that its free end can find a matching primer, located on the surface. We used Brownian dynamics simulations (with a united-atom model) to model the basic kinetics of an SPA experiment. The simulations mimic the temperature cycles and the molecule duplication process found in SPA. Our results indicate that the steric interaction between molecules leads to a decreased duplication probability for molecules in the center of a colony and to an outward leaning for the molecules on the perimeter. These effects result in slower amplification (compared to solution PCR) and indicate that steric interaction alone can explain the loss of the exponential growth (characteristic of solution PCR) of the number of molecules in an SPA experiment. Furthermore, the growth of the colony as a function of the number of thermal cycles is found to be similar to the one obtained with a simple Monte Carlo simulation