Hybridization interactions of surface-bound DNA duplexes is central to microarray sensors, and the presence of a particular sequence can be determined via fluorescence microscopy.  In some cases, perfectly complementary sequences are measured as dimmer than those with single mutations.  To investigate this phenomenon, both perfectly complementary and mismatched DNA oligomer sequences were investigated with Monte Carlo molecular simulation using a coarse-grained DNA model together with a newly-developed fluorescent label model.  Duplexes were studied both in solution and surface-bound as a function of temperature, and results were analyzed in terms of both energetic and structural properties.

DNA mutation and fluorescent label effects in surface-bound 25mer microarrays: Molecular simulation of bright mismatches

253rd National Meeting (2017)

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