Long-term reduction in poly(dimethylsiloxane) surface hydrophobicity via cold-plasma treatments.

Poly(dimethylsiloxane), PDMS, a versatile elastomer, is the polymer of choice for microfluidic systems. It is inexpensive, relatively easy to pattern, and permeable to oxygen. Unmodified PDMS is highly hydrophobic. It is typically exposed to an oxygen plasma to reduce this hydrophobicity. Unfortunately, the PDMS surface soon returns to its original hydrophobic state. We present two alternative plasma treatments that yield long-term modification of the wetting properties of a PDMS surface. An oxygen plasma pretreatment followed by exposure to a SiCl4 plasma and an oxygen-CCl4 mixture plasma both cause a permanent reduction in the hydrophobicity of the PDMS surface. We investigate the properties of the plasma-treated surfaces with X-ray photoelectron spectroscopy (XPS) and contact angle measurements. We propose that the plasma treated PDMS surface is a dynamic mosaic of high- and low-contact-angle functionalities. The SiCl4 and CCl4 plasmas attach polar groups that block coverage of the surface by low-molecular-weight groups that exist in PDMS. We describe an application that benefits from these new plasma treatments, the use of a PDMS stencil to form dense arrays of DNA on a surface.

Microdisplacement printing.

We describe a new patterning technique that employs microcontact printing to replace preformed labile self-assembled monolayers (SAMs) selectively; we call this "microdisplacement printing". We demonstrate that this technique results in ordered molecular regions of both the patterning ("displacing") molecule as well as the remnant labile film, here 1-adamantanethiolate. The existence of the 1-adamantanethiolate SAM before patterning hinders lateral surface diffusion of the patterning molecules, and therefore permits the use of molecules that are otherwise too mobile to pattern by other methods.

Progress toward demonstration of a surface based DNA computation: a one word approach to solve a model satisfiability problem.

A multi-base encoding strategy is used in a one word approach to surface-based DNA computation. In this designed DNA model system, a set of 16 oligonucleotides, each a 16mer, is used with the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in eight central variable ('v') base locations, and the remaining fixed ('F') base locations are used as a word label. The detailed implementations are reported here. In order to achieve perfect discrimination between each oligonucleotide, the efficiency and specificity of hybridization discrimination of the set of 16 oligonucleotides were examined by carrying out the hybridization of each individual fluorescently tagged complement to an array of 16 addressed immobilized oligonucleotides. A series of preliminary hybridization experiments are presented and further studies about hybridization, enzymatic destruction, read out and demonstrations of a SAT problem are forthcoming.

Surface-based DNA computing operations: DESTROY and READOUT.

DNA computing on surfaces is where complex combinatorial mixtures of DNA molecules are immobilized on a substrate and subsets are tagged and enzymatically modified (DESTROY) in repeated cycles of the DNA computation. A restriction enzyme has been chosen for the surface DESTROY operation. For the READOUT operation, both cycle sequencing and PCR amplification followed by addressed array hybridization were studied to determine the DNA sequences after the computations.