Studies of patterned surfaces for biological microarrays

Over the past 10 years, biological microarrays have developed into an invaluable tool for genetic and protein research. The task to draw meaningful conclusions between variations of genes and their expression requires millions of comparisons between standard and stressed samples, usually the cDNA, RNA, or proteins within cells. For such a project, high-information-density, highly pure arrays are required. In fabricating an array on a uniform or an unpatterned substrate, droplets of solution, if placed too closely, can bleed into each other and can cross-contaminate several array sites. Therefore, a uniform surface limits the density of droplets that can be placed to create an array. When the surface is patterned with a barrier between the droplets, then the density of array sites can be significantly larger (uniform surface, ∼200–500μm center-to-center; patterned surface, 100μm center-to-center and less with present loading technology). We have explored the patterning of surfaces to construct biological microarrays, via altering the surface chemically to create array sites with gold-thiol chemistry, and via a template placed on the surface to outline the elements. In the template strategy, we have investigated poly(dimethyl siloxane) (PDMS) films (5–10μm) with holes in a regular array. However, the hydrophobic PDMS repels water to such an extent that the droplets do not wet the template and cannot travel down the wall of the PDMS hole to interact with the surface. As a consequence, if not accurately placed in the array sites, they also do not load into the holes to form filled features. Our current studies focus on altering the surface of the PDMS to allow the droplets to fall into the PDMS holes. To alter the surface and not the bulk, we have experimented with plasma chemistry. To create a temporary contact angle change, oxygen plasma has been employed. However, the PDMS recovers and reverts to it characteristically hydrophobic surface. When we expose PDMS to oxygen and then to SiCl₄ or to CCl₄ plasma, the surface change becomes long-lasting. The new plasma treatments allows for increased control over wetting properties of the PDMS material, which is key to our investigations into biological applications of PDMS. In our characterization of the plasma treatments, we have found new insights into the role of low-molecular-weight-groups of PDMS in the recovery of the contact angle over time. Contact angle data show a Langmuir isotherm curve, and coupled with XPS, AFM and ATR-FTIR studies, we have characterized the plasma-treated PDMS samples and the wetting behavior evolution over time. Using the behavior of plasma-treated PDMS, we have created DNA features as small as ∼1.1μm.