This paper reviews methods for forming micropatterned surfaces of self-assembled monolayers of alkylthiolates on gold and their use in studying and manipulating interactions of biological systems with solid surfaces. Optics-based biosensor arrays are an example of a technology where it is desirable to prepare microscopic patterns of well-defined surfaces that contain regions with specific bioactivity or that resist nonspecific biointeraction (e.g., nonspecific protein adsorption and cellular attachment). Several simple patterning techniques are described including photopatterning, monolayer displacement, microinjection, and electrochemical patterning. The relative merits of these techniques are discussed with regard to maintenance of bioactivity of immobilized chemical species, resistance to nonspecific bioactivity, and application to rapid, large- scale patterning. The use of electrochemical patterning is also described in the creation of a model microsensor array.

The development of techniques which can be used for the discrete immobilization of multiple antibodies on solid supports has important applications in the areas of clinical diagnostics, drug discovery, and biosensor development. While photolithography has provided many elegant methods for generating spatially resolved reactive surface functionalities, the problem of nonspecific adsorption of proteins which occurs during sequential immobilization steps continues to hamper the development of antibody sensing arrays. This nonspecific adsorption prevents the establishment of unique and individually addressable binding sites on the substrate surface. In an effort to solve this problem, we have synthesized and characterized a series of photoactivatable silanes which can be used for the light- directed attachment of antibodies to solid supports. These compounds produce amine-reactive functional groups upon irradiation with UV light. The first silane derivative prepared yielded a relatively hydrophobic surface when it was used for substrate modification. The resultant surface exhibited a high degree of nonspecific protein adsorption even in the absence of light activation. We therefore decided to synthesize a more hydrophilic analog. This second derivative displayed low nonspecific protein binding even in the absence of detergents or protein blocking agents. We have used this second compound to discretely immobilize four different IgG antibodies (each directed against a different antigen) on several hydroxyl-bearing substrates. Antigen binding experiments using fluorescent and ¹²⁵I-labeled antigens have confirmed that the immobilized antibodies retain their functionalities.

We have demonstrated that covalently immobilized enzyme can be used to chemically modify and pattern a chemisorbed peptide film on a solid substrate. The enzyme, alpha- chymotrypsin, was covalently attached to silica and latex spherical beads by glutaraldehyde crosslinking to an amino surface functionality. The fluorescent peptide, suc-ala-ala- phe-AMC (SAAP-AMC) was immobilized to an aminosilane- modified flat silica surface by forming an amide bond to its free carboxylic acid group. SAAP-AMC surfaces were characterized using water wetability, fluorescence spectroscopy and x-ray photoelectron spectroscopy. Upon attack by alpha-chymotrypsin coated beads, the fluorescent AMC group (325 nm ex, 395 nm em) is cleaved from the SAAP- AMC peptide surface and a red-shift occurs in the AMC fluorescence providing a standard marker for enzymatic activity (345 nm ex, 440 nm em). Thus, the signature for alpha-chymotrypsin bead activity against the surface is a reduction in fluorescence intensity from the peptide surface (at 395 nm) and a concomitant increase in fluorescence in the solution above the surface (at 440 nm). Treatment of the SAAP-AMC silica surfaces with alpha-chymotrypsin-beads showed a reduction of the surface fluorescence to background in less than 24 hours, with a corresponding increase of free AMC fluorescence in solution. By restricting the contact region of the beads with the peptide surface we were able to demonstrate chemical patterning of the peptide surfaces.

A standard semiconductor process and a chemical immobilization of the functional groups to the glass surface were used to fabricate the biocompatible base substrates for the cell biosensor with specific micropatterns of amine groups and, thereby to create the extracellular protein island of the defined shape and size that support a single cell attachment. Defined size, 15 - 100 micrometer in each side, of rectangular pattern was obtained by the bulk- etching of n-type [100] Si wafer. After etching process of glass with concentrated HNO₃, the glass substrate covered with the silicon mask was exposed to hexamethyldisilane vapor at 200 degrees Celsius for 30 minutes to couple the silane. Human umbilical vein endothelial cells were cultured on the micropattern after crosslinking the human fibronectin to micropatterned silane. It was possible to adhere endothelial cells in a predetermined location and shape with this technique. The responsibility of adhered endothelial cells to physical stress, such as blood flow, was limited by the controlling the polymerization of actin cytoskeleton and morphology of the cell. The simple laminar flow chamber was developed to exposure defined laminar shear stress on the micropatterned endothelial cell array. Fabrication of biocompatible micropattern with this method is experimentally simple and highly reproducible for application of the cell biosensor for physical and chemical applications.

To assess the effect of surface topography on cell attachment, central nervous system (astroglial cells) cells were grown on surfaces patterned with two different types of texture. Reactive ion etching (RIE) was used to induce nanometer-scale roughness in silicon wafers. In a subsequent wet etch, photo-patterned resist protected selected areas of the surface, resulting in a pattern of modified and unmodified texture. Scanning electron microscopy (SEM) showed that the RIE-roughened 'primary' surface consists of randomly positioned columnar structures (diameter approximately equals 50 nm, height approximately equals 250 nm). The wet-etched 'secondary' surfaces had shorter and more sparsely distributed projections, controlled to a degree by wet etch duration. Confocal microscopy and SEM demonstrated that transformed astroglial (LRM55) cells preferred secondary surfaces. The morphology of cells on secondary surfaces depended on wet etch duration. with brief wet etch, cells hade stellate or mounded morphology and were not closely adherent to the surface. With long wet etch, cells had an epithelial-like morphology and were closely adherent to substrates. Under all conditions, cells discriminated between primary and secondary surfaces. In contrast to LRM55 cells, astrocytes in primary cell culture preferred primary surfaces. Thus changes in surface topography produce cell-specific selectivity and change cell attachment characteristics.

A new approach in nanostructure technology particularly in the functionalization of surfaces has been developed on the basis of crystalline bacterial cell surface layers (S- layers). S-layers are composed of monomolecular arrays of identical (glyco)proteins showing high molecular order, defined mass distribution and isoporosity, and a high binding capacity for functional macromolecules. The possibility for recrystallizing isolated S-layer subunits into large isoporous, coherent lattices at solid supports, at the air/water interface or on lipid films and for handling such layers by standard Langmuir-Blodgett techniques opens a broad spectrum of applications in basic and applied membrane research. S-layer supported functional phospholipid bilayers or tetraether lipid films mimic the molecular architecture of those archaebacterial cell envelopes that are exclusively composed of an S-layer and a plasma membrane. This novel concept could lead to new techniques for exploiting large scale structural and functional principles of membrane associated and integrated molecules (e.g. ion channels, proton pumps, receptors).

Sandia National Laboratories has recently opened the Chemical and Radiation Detection Laboratory (CRDL) in Livermore, Calif. to address the detection needs of a variety of government agencies (e.g., Department of Energy, Environmental Protection Agency, Department of Agriculture) as well as provide a fertile environment for the cooperative development of new industrial technologies. This laboratory consolidates a variety of existing chemical and radiation detection efforts and enables Sandia to expand into the novel area of biochemically based sensors. One aspect of our biosensor effort is further development and optimization of enzyme modified field effect transistors (EnFETs). Recent work has focused upon covalent attachment of enzymes to silicon dioxide and silicon nitride surfaces for EnFET fabrication. We are also investigating methods to pattern immobilized proteins; a critical component for development of array-based sensor systems. Novel enzyme stabilization procedures are key to patterning immobilized enzyme layers while maintaining enzyme activity. Results related to maximized enzyme loading, optimized enzyme activity and fluorescent imaging of patterned surfaces are presented.

This paper presents a new method for obtaining highly efficient electrochemiluminescence (ECL) of tris(2,2'- bipyridine) ruthenium (TBR) in aqueous solutions and a biosensor which utilizes this method. An interdigitated, microelectrode array is employed with electrode widths and spacings of 5 micrometer. The microelectrode is supported on a silicon nitride coated silicon substrate and occupies 1 mm². Each microelectrode is 1 mm long and 5 microns wide. The diffusion enhancement produced by the microelectrode geometry, the small electrode spacing and the electrode material are all critical parameters for high ECL efficiency. ECL has been detected from TBR concentrations as low as 1 (mu) M, using a silicon PIN photodiode detector at room temperature. For biosensing applications, TBR is attached to the molecule of interest and ECL is then generated at the electrode surfaces. Cell configuration and the results of preliminary studies of the detection of TBR labeled DNA, attached to paramagnetic beads are presented.

A micromachined optical 'trap' to capture and move micron sized dielectric particles is presented. The trap consists of four single mode optical fibers mutually aligned to have a common optical beam intersection at the center of a micromachined housing. The intersection of the beams forms an optical 'cross-hair' which captures dielectric microparticles with a strong optical gradient force field, and holds them for further manipulation, visualization, and/or analysis. The stability and magnitude of the trapping force fields are comparable to the single beam 'optical tweezers' technique, but are considerably more versatile.

Miniature spectrometers were demonstrated by mounting micromachined diffraction gratings onto CCD imaging devices. Two implementations were tested: one for high dispersion and high sensitivity applications, and the other for low-cost consumer applications. The first system showed a dispersion of 1.7 nm/pixel and a resolution of 74.4 for the bandwidth of interest. The free spectral range of these devices was designed to be in the visible range for this particular application. The diffraction efficiency of the system was 63%. The second, low-cost system demonstrated a dispersion and resolution of 2.55 nm/pixel and 69.8 respectively. These specifications are comparable to that of a conventional, low-end commercial spectrometer. Results are shown for their applications in biochemical analysis. Optimization was sought by adding micromachined lenses and creating specialized, computer generated gratings to compress and shape the spectral signal.

Traditionally microscale measurements of pH are based on potentiometric measurements with a pH glass microelectrode. The preparation of these electrodes is, however, very time consuming. We developed pH micro-optodes for use in seawater in the range of pH 7 - 9. The optodes are based on immobilized acid-base indicators, which change their color and/or fluorescence properties as a function of the pH. Various dyes were immobilized directly on the tip of a tapered optical fiber by different techniques. We then investigated these pH optodes with respect to response time, mechanical stability and calibration characteristics. Dependent on the optical properties of the indicator material we used different light emitting diodes (LEDs) as the light sources and either a photodiode or a photomultiplier as detector.

In this paper the fabrication and test of a microfluidic system integrated with optical waveguide and photodiode circuits on the same silicon chip are presented. A chemical reaction taking place in the miniature flow channels, which form a simple chemical distribution system on chip is detected by the photodiodes receiving light transmitted via the optical waveguide circuit. Reactions which cause either a change in absorbance or luminescence have been employed in the studies made. The mesa photodiode structures are butt coupled to the multilayer glass optical waveguides and have integral quantum efficiencies of approximately 80%, responsivities of about 0.5 and a broad spectral response. Anisotropic etching of the {100} silicon in a KOH solution is used to form these highly efficient mesa photodiodes. The buried optical waveguide structures, which are formed in low loss (0.5 dB/cm) germanium doped core glass, couple very effectively to the mesa diodes. Light is coupled to the waveguides via an optical fiber which is fastened to the chip by means of a simple connector etched into the silicon. Fluids are transported to and from the chip by means of quartz capillaries similarly fastened to the chip by means of integrated connectors.

Microfabricated fluidic systems allow complex chemical analyses to be performed on sub-nanoliter volumes of sample. Compared to macroscopic systems, these devices offer many advantages, including the promise of performing some analytical functions more rapidly and on smaller samples. However, miniaturization of analytic instruments is not simply a matter of reducing their size. At small scales, different effects become more prominent, rendering some processes inefficient and others useless. The small scales also permit the creation of novel devices, such as the H- filter, which we are using to extract analytes from whole blood. Fluid flow in microfluidic systems is entirely dominated by viscous forces, making diffusion the sole mechanism of mixing. In addition, a larger fraction of molecules are lost to surface adsorption as devices shrink. This paper examines some of the issues involved in device miniaturization, specifically those phenomena that become increasingly dominant.

A new silicon filter with straight filtration channels has been fabricated and characterized. The semi-permeable membrane of the filter is made of a sandwiched p⁺ polysilicon/oxide/p⁺ silicon structure. The sacrificial oxide between the two silicon layers determines the pore size of the filter. This filter can be mass produced and has very precise control over filtration channels (variation less than 25%). Two log reduction of 100 nm fluorescent particles has been achieved in our 50 nm filters. The tested filtration fluxes for filtered DI water, 0.1 M PBS and ethanol solution (75% wt) were 0.54 - 1.5, 0.10, 0.54 - 1.2 ml/cm²hr, respectively.

The fabrication and characterization of a microfabricated, fexural plate, acoustic wave delay line is presented for use in the physical translation of fluids and/or biological cells. The device consists of dual interdigitated transducers patterned on a thin film composite membrane of silicon nitride, platinum, and sol gel derived piezoelectric ceramic (PZT). The acoustic properties of the device are presented along with preliminary applications to mechanical transport and liquid delivery systems. Improved acoustic signals and improved mass transport are achieved with PZT over present fexural plate wave devices employing ZnO as the piezoelectric material.

A unique ektacytometer for monitoring blood cell deformability constructed using a silicon and glass microfabricated flow cell, a diode laser source and CCD detector, is presented. The device described in this paper relies on the reflection of the incident laser beam from the silicon surface, and hence does not act as a transmission cell. In this sense the device is compatible with other microfabricated devices which also utilize a reflection based optical geometry. Flow induced changes in the diffraction pattern generated by blood samples flowing through the microfabricated cell, and passing through the laser beam, are analyzed and compared with expected results based on shear induced changes in erythrocyte (red blood cell) shape within the flow cell. Finally, optimization of the flow cell design, and possible applications toward biomedical instrumentation are also discussed.

A number of computational and experimental studies on flows in venular bifurcations have concentrated on the distribution of blood components and the formation of a 'separation surface' between two converging flows with different red blood cell concentrations and viscosities. To better understand these phenomena, we have used microfabrication techniques to construct artificial venular bifurcations with physiologically realistic dimensions. The current apparatus consists of a single bifurcation formed from tubes with semicircular cross sections of radius 50 (mu) . The vessels are fabricated from two glass slides using an abrasive etching process and a low melting point glass as sealant. Using a laser scanning confocal microscope, we have obtained the first three-dimensional images of flow structures in microscopic vessels; in particular we have imaged the separation surface for converging Newtonian fluids. A quantitative comparison is made between finite element simulations and experimental results of the position of the separation surface for different inlet flow ratios. Computed positions of the separation surface at the mid- depth of the outlet branch are in excellent agrement with experiment results obtained by confocal microscopy.

The purpose of this study was to develop a miniaturized CO- oximeter for hemoglobin derivative measurement using microfabrication technology. A microcuvette (volume equals 507 nl) was fabricated for analysis of percent oxyhemoglobin (O₂Hb%) in whole blood. A cuvette of 50 micrometer pathlength produced optimal absorbance sensitivity to changes in O₂Hb%. The pressure differential for a nominal blood flow rate of approximately 1 microliter/second was 4.1 kPa (16.6 in water, 0.6 psi). Entrained bubbles were easily discharged at these pressures. Spectral measurements were made using an ocean optics miniaturized spectrophotometer (500 - 700 nm). A fiber optic probe with one receiving and six emitting fibers (200 micrometer core and 0.22 NA) was used for spectral measurement. Heparinized fresh blood from a healthy volunteer was tonometered with N₂, CO₂, and O₂ mixtures to produce six samples with O₂Hb% from 22 - 97%. Chemometrics was used for data analysis. The second derivatives of spectra were taken to eliminate baseline changes caused by RBC light scattering. Indirect calibration by principal component regression was applied to the second derivative. Four factor cross validation showed a correlation coefficient of 0.9994 between measured O₂Hb% of lysed blood using an OSM3 CO- oximeter (Radiometer America, Ohio) and whole blood using the microfabricated cuvette. The linear relationship is: O₂Hb%micro-cuvette equals 0.8411% plus 0.9882 multiplied by O₂Hb%_OSM3. We conclude that O₂Hb% measurement on unlysed whole blood using a silicon microfabricated cuvette is practical and that results are similar to traditional CO- oximetry.

Microgrooves (width 6, 7, and 8 micrometer, each with length 20, 30, and 40 micrometers, respectively; depth 4.5 micrometers; number 4704 in parallel of one size per chip; chip dimensions 12 multiplied by 12 mm) photofabricated in the surface of a single-crystal silicon substrate were converted to leak-proof microchannels by tightly covering them with an optically flat glass plate. Using the microchannels as a model of physiological capillaries, total flow rate of heparinized whole blood taken from healthy subjects was determined under a constant suction of 20 cmH₂O, while flow behavior of blood cells through individual channels was microscopically observed. The apparent viscosity (ratio to that of saline) of whole blood was obtained as 4.7 plus or minus 0.5, 3.7 plus or minus 0.3, and 3.4 plus or minus 0.2 (mean plus or minus SD, n equals 4) for 6, 7, and 8 micrometer width channels, respectively. Normal leukocytes passed, showing a round shape, through the channels much more slowly then erythrocytes, but caused no appreciable interference with passage of erythrocytes. Meanwhile, cells exposed to the chemotactic peptide FMLP (1 - 10 nM) and bacterial cells (Escherichia coli K 12; 6 multiplied by 10⁶/ml) slowed further greatly, showing very irregular shapes, and eventually blocked the channels. Such a response of leukocytes took place immediately after the exposure to FMLP, but it appeared gradually with time after the exposure to the cells.

Microfabricated electro-optical-mechanical systems are expected to play an important role in future biomedical, biochemical and environmental technologies. Semiconductor photonic materials and devices are attractive components of such systems because of their ability to generate, transmit, modulate, and detect light. In this paper we report investigations of light-emitting semiconductor/glass microcavities filled with simple fluids. We examine surface tension for transporting liquids into the intracavity space and study the influence of the liquid on the spectral emission of the microcavity.

The marriage of microfabricated materials with microbiological systems will allow advances in medicine to proceed at an unprecedented pace. Biomedical research is placing new demands on speed and limits of detection to assay body tissues and fluids. Emerging microfabricated chip technologies from the engineering community offer researchers novel types of analysis of human samples. In guiding these developments, the ability to swiftly and accurately gain useful information for identification and establish a diagnosis, is of utmost importance. Current examples of such technology include DNA amplification and analysis, and fluorescent cell analysis by flow cytometry. Potential applications include the development of rapid techniques for examining large number of cells in tissue or in blood. These could serve as screening tools for the detection and quantification of abnormal cell types; for example malignant or HIV infected cells. Micro/nanofabrication methods will make these devices compact, providing access of this technology to point of care providers; in a clinic, ambulance, or on a battlefield. Currently, these tools are in the construction phase. Upon delivery to researchers, validation of these instruments leads to clinical demand that requires approval from the Food and Drug Administration. This paper outlines criteria that successful devices must satisfy.

We demonstrate a novel hydrodynamic shear activation of leucocyte adhesion, using physiological flow conditions and a microfabricated array of channels with length scales similar to those of human capillaries. Vital chromosome stains and cell specific fluorochrome labeled antibodies reveal that the eventual adhesion of the leukocytes to the silicon array displays a strong dependence on cell type and nuclear morphology, with granulocytes activating more rapidly with distance and penetrating a smaller distance than lymphocytes. Further, the granulocytes interact with the lymphocytes in a self-exclusionary manner under shearing flow with the eventual separation of the two cell types in the array. Such arrays of microfabricated obstacles thus have an interesting potential for sorting white blood cells by type from a 10 microliter drop of whole blood.

Immune rejection rapidly destroys cellular transplants, particularly xenografts. Encapsulation of xenografts with an artificial membrane has been proposed as a means of cell immunoprotection after transplantation. Currently, organic biocapsule materials are used in this context, and have presented significant problems that relate to capsule biodegradation and limited biocompatibility. In this review, we describe our alternative approach to immunoisolation using microfabricated biocapsules. Previous studies have shown the viability and functionality of various cell lines within our biocapsule microfabricated environment. This review describes general cell culture wafer and biocapsule fabrication protocols, as well as, in vitro studies on the viability and functionality of pancreatic islets of Langerhans in microfabricated culture wafers and biocapsules.

The ability to easily monitor the rate of cell growth has many useful applications such as characterizing cell lines to optimize growth conditions and compound screening to test for cytotoxicity. As a cell growth sensor, the ultrasonic flexural plate-wave device offers a convenient assay that is non-invasive, continuous, and capable of full automation for high throughput screening. The flexural plate-wave (FPW) device is a microfabricated sensor consisting of a thin silicon nitride membrane with aluminum and zinc oxide transducers at both ends. These interdigitated transducers send and receive acoustic plate waves that propagate along the membrane. Applications of the device include mass sensing, achieved by measuring the frequency shift caused by mass loading of the membrane, and pumping of liquids and gases. We have conducted studies that established the biocompatibility of the FPW device materials with cell cultures. In addition, biological samples were exposed to the ultrasonic agitation of the device and no damaging effects were found. Experiments were performed using the FPW device to sense cell growth for mammalian suspension (non- adherent) cells. Results show a good correlation between change of cell number and frequency.

The use of microchips for performing biochemical processes has the potential to reduce reagent use and thus assay costs, increase throughput, and automate complex processes. We are building a multifunctional platform that provides sensing and actuation functions for a variety of microchip- based biochemical and analytical processes. Here we describe recent experiments that include on-chip dilution, reagent mixing, reaction, separation, and detection for important classes of biochemical assays. Issues in chip design and control are discussed.

A mechanical interlock system is reported that achieves the manual alignment of two components accurate to within plus or minus 10 micrometers in three spatial coordinates. In addition, the system allows rapid component interchange. The system is based on a novel two stage application of the principles of the kinematic location of instrument components. A macro scale kinematic mount allows manual handling while a micro scale mount delivers the accuracy required. Silicon microfabrication methods are used to create features in the micron size range accurately and repeatable for the micro scale mount. Such a system could be used for fluidic, pneumatic, electrical, optical, or mechanical interconnects. We use it for the alignment of optics to flow channel in an optical flow cytometer which is part of a microfluidic total chemical analysis system we are developing.

Microfabricated channels are widely thought to be the key to realizing chemical analysis on a microscopic scale. Chemical and biological information in the microchannels is often probed with optical techniques such as fluorescence, Raman and absorption spectroscopy. However, the optical effects of a microchannel are not well characterized. For example, it is important to understand the optics of the channel in order to optimize optical coupling efficiency. We consider various designs for enhancing the sensitivity of fluorescence detection in a microchannel.