This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.104.051904v1 89/1/32    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Mercier, J.-F. Articles by Slater, G. W. Search for Related Content PubMed PubMed Citation Articles by Mercier, J.-F. Articles by Slater, G. W.

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

Department of Physics, University of Ottawa, Ottawa, Ontario, Canada

Correspondence: Address reprint requests to J.-F. Mercier, E-mail: jmercier{at}physics.uottawa.ca; or G.W. Slater, E-mail: gslater{at}science.uottawa.ca.

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 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.