Keywords

Free energy landscapes, Molecular simulations, Chemical thermodynamics, DNA microarrays, Transition state, Medical fields, Nucleotides, Coarse-grain model, DNA hybridization, Statistical thermodynamics

Abstract

DNA microarrays are a potentially disruptive technology in the medical field, but their use in such settings is limited by poor reliability. Microarrays work on the principle of hybridization and can only be as reliable as this process is robust, yet little is known at the molecular level about how the surface affects the hybridization process. This work uses advanced molecular simulation techniques and an experimentally parameterized coarse-grain model to determine the mechanism by which hybridization occurs on surfaces. The results show that hybridization proceeds through a mechanism where the untethered (target) strand often flips orientation. For evenly lengthed strands, the surface stabilizes hybridization (compared to the bulk system) by reducing the barriers involved in the flipping event. For unevenly lengthed strands, the surface destabilizes hybridization compared to the bulk, but the degree of destabilization is dependent on the location of the matching sequence. Taken as a whole, the results offer an unprecedented view into the hybridization process on surfaces and provide some insights as to the poor reproducibility exhibited by microarrays.

Original Publication Citation

T. J. Schmitt, J. B. Rogers, and T. A. Knotts IV, Exploring the Mechanisms of DNA Hybridization on a Surface, J. Chem. Phys., 138, 035102 (2013).