DNA microarrays, chips in which unhybridized single stranded DNA molecules (probes) are bound to a surface and used as detectors for their complementary strands (targets), have received interest for a variety of applications including disease diagnosis and specified genotyping. However, current limitations of this technology can lead to both false positive and false negative results. To better understand the DNA hybridization interactions under these conditions, Monte Carlo molecular simulations using a coarse-grained model for DNA were carried out for both solution and surface-bound environments. When multiple strands are bound to a surface, new duplex � duplex interactions are introduced, which can affect probe-target hybridization. These interactions are shown to be dependent on probe surface density, and probe placement, sequence, and length are varied to study their effects on hybridization stability. Results are analyzed for hydrogen-bonding patterns as a function of these variables, as well as their effects on hybridization energies.

Effect of probe density on DNA hybridization in microarrays: A Monte Carlo simulation study

245th National Meeting (2013)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.