Off-lattice simulation of the solid phase DNA amplification

Recent simulations of the solid phase DNA amplification (SPA) by J.-F. Mercier et al. [Biophys. J. 85 (2003) 2075] are generalized to include two kinds of primers and the off-lattice character of the primer distribution on the surface. The sigmoidal character of the primer occupation by DNA, observed experimentally, is reproduced in the simulation. We discuss an influence of two parameters on the efficiency of the amplification process: the initial density p0 of the occupied primers from the interfacial amplification and the ratio r of the molecule length to the average distance between primers. The number of cycles required for a complete saturation decreases with p0 roughly as p0−0.26. For r=1.5, the number of occupied primers is reduced by a factor two, when compared to the case of longer molecules. Below r=1.4, the effectivity of SPA is reduced by a factor 100.