Heterogeneous DNA hybridization, with one strand immobilized on a surface, is important to understand because of its role in the functioning of DNA microarrays.  The effect of surface density and location of binding sites on the hybridization and hydrogen bonding pattern of a DNA undecamer was studied for two different sequences using a coarse-grained model and Monte Carlo molecular simulation.  The results indicate destabilization of hydrogen bonding interactions dependent on a base's location in the sequence.

Monte Carlo molecular simulation of surface binding density effects on DNA hybridization of two undecamer sequences

247th National Meeting (2014)

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