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, observe...

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Bibliographic Details
Published in:Computer physics communications 2005-08, Vol.170 (2), p.131-136
Main Authors: Krawczyk, M.J., Kułakowski, K.
Format: Article
Language:English
Subjects:
Amplification
Chips
Computer simulation
DNA
Spatial distribution
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Summary: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 p 0 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 p 0 roughly as p 0 −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.
ISSN:0010-4655
1879-2944
1386-9485
DOI:10.1016/j.cpc.2005.03.108