AVS 50th International Symposium
    Biomaterial Interfaces Wednesday Sessions
       Session BI-WeP

Paper BI-WeP13
Molecular Simulation of Mixed SAMs Including Thiolated DNAs on Gold (111) Surfaces

Wednesday, November 5, 2003, 11:00 am, Room Hall A-C

Session: Poster Session
Presenter: J.P. Sullivan, University of Washington
Authors: J.P. Sullivan, University of Washington
S. Jiang, University of Washington
Correspondent: Click to Email
The ability to tether DNAs to a solid support has yielded a variety of practical technologies including DNA microarrays and DNA based biosensors. Yet in spite of the rapid advances of surface tethered DNAs in biotechnological applications, improvements to these technologies are made through a painstaking combinatorial process that suffers from a lack of mechanistic understanding. It has been shown that the hybridization of ssDNA SAMs can be affected by the introduction of a non-DNA terminated thiol as a diluent. Experimentalists in our group, for example, are using oligo-ethylene glycol (OEG) terminated thiols along with thiolated ssDNA to form mixed SAMs on gold (111). Speculation has been unable to yield a predictive tool for which diluent length and density will have the best impact on a given DNA probe. Accordingly, we turned to simulation to provide atomic resolution images of these mixed SAMs, revealing information that could not be intuited. All simulations were carried out in explicit solvent with Na+ to balance charge, and NaCl to control ionic strength. The CHARMM27 all-atom potential force field was used to model the DNAs, while the TIP3P potential was used for water interactions. The OEGs were treated using a SJY force field with demonstrated accuracy for OEG-thiols. We present results for the packing of pure DNA SAMs (both single and double stranded, of varying sequence lengths and compositions, and at different ionic strengths). The pure SAM packing results were then used to set up simulations of DNA SAMs mixed with oligo-ethylene glycol at varying diluent lengths (number of repeat units) and densities, for which results are also reported. These results will be instrumental in developing theory-based methods for selecting diluents and diluent densities. This will reduce or eliminate the trial and error process involved in determining diluent properties for the countless possible DNA probes that do not already have optimized diluents.