BIOPHYSICAL THEORY AND MODELING |
Solid Phase DNA Amplification: A Brownian
Dynamics study of crowding effects
Jean-Francois Mercier 1 and Gary W Slater 1*
1 University of Ottawa
* To whom correspondence should be addressed. E-mail: gslater{at}science.uottawa.ca.
Submitted on August 31, 2004
Revised on October 14, 2004
Accepted on 24 March 2005
 |
Abstract |
|---|
Solid 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 sucessfully 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 a 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 a 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.
Key Words:
Brownian Dynamics, DNA Bending, DNA duplication, DNA dynamics, Grafted DNA, Solid Phase DNA Amplification
