Research Tools : Arrays


Hydrogel Arrays for Screening Cell-Substrate Interactions, Now in Multiwell Format

Building on their previous work, the researchers have now adapted their method to any commercially available, glass or polystyrene-bottom multiwell plate. In the new process, hydrogel is covalently immobilized to the bottom of each well and then selectively polymerized. In this way the spots are completely isolatable, allowing for systemic and independent control of their chemical composition and XYZ physical dimensions.

Once the hydrogel array is formed, each of the spots can be exposed to different soluble factors without risk of diffusion.

Controlling the Formation of Stem Cell Colonies with Tailored SAM Array

Building on their previous work, the researchers have developed a new feature to make SAM arrays an even better tool to control cell aggregation. Specifically, the spots on the array consist of cellular adhesive peptides stuck to the surface by an easy-to-cleave labile bond. The peptides enable layers of cell to form and detach from the array without scraping or other external manipulation.

Any peptide capable of forming such a bond (e.g., a thioester bond) with the SAM surface could be employed.

Hydrogel Arrays for Screening Cell-Substrate Interactions

UW–Madison researchers developed a new method for forming patterned hydrogel arrays featuring any number of test spots possessing different characteristics, such as shape and chemical composition. The arrays can be used to culture a range of cell types and rapidly analyze their behavior (e.g., attachment, spreading, proliferation and differentiation).

The arrays are prepared using a hydrogel precursor solution containing a polymer and crosslinker. The solution is sandwiched between stenciled SAM layers containing hydrophilic (‘water-loving’) and hydrophobic (‘water-hating’) regions, then polymerized and released.

As a result of the process, the array features hydrophilic spots surrounded and isolated by hydrophobic regions, preventing any mixing of contents. The spots can have any desired shape, size and chemical composition.

Assembly of Full-Length Genes from DNA Arrays

UW–Madison researchers have developed a method to produce full-length genes using RNA intermediaries that are produced by run-off transcription from DNA array features. Specifically, an RNA polymerase promoter is appended to the surface-bound oligonucleotides. RNA copies are produced using T7 RNA polymerase and then self-assembled into full RNA transcripts by hybridization and ligation. The RNA transcripts can readily be converted into their corresponding genes using RT-PCR (reverse transcription polymerase chain reaction). These genes then may be employed to express the encoded protein of interest.

Investigating Cell-Surface Interactions via Chemical Array

UW–Madison researchers have developed an improved approach to SAM-based experiments using simple methods to construct arrays of SAMs that can be used to rapidly investigate how selected types and densities of ligands impact cell behaviors such as adhesion, spreading, proliferation, migration and differentiation.

The substrate comprises a slide coated with metal such as gold onto which a polymer stencil is fitted. Through small holes in the stencil, alkanethiol solutions are deposited, forming micrometer-sized spots (up to 120 or more) of SAM. During this deposition process, a range of biological molecules can be tethered to each SAM spot (at varied densities and mixtures), allowing researchers to examine a wide range of possible biological ligands on a single surface. Furthermore, arrays formed using alkanethiolates that prevent biofouling allow researchers to carefully examine the effects of a particular ligand on the behavior of cells cultured on each array spot. Importantly, array fabrication and subsequent examination of cell behavior can be carried out using tools that are standard in biological laboratories such as pipettes and light/fluorescent microscopes.

Using UV Light to Functionalize Metal Oxides for Use in Biosensors, Solar Cells and Other Devices

UW-Madison researchers have developed methods for functionalizing metal oxides, including TiO2, with organic molecules.  The methods use UV light to covalently bond linker precursors to the surface of a metal oxide.  Then other molecules, such as dye molecules or biomolecules like DNA, can be coupled to the linker precursors to further functionalize the metal oxides. 

The functionalized oxides may be used alone or as coatings on various substrates.  They can be incorporated into devices such as biosensors or dye-sensitized solar cells. 

These methods provide functionalized metal oxides with higher densities of organic molecules and greater thermal and chemical stability than functionalized metal oxides prepared using conventional methods.  In addition, these methods do not require high temperatures or an ultra high vacuum, and are simpler and more reproducible than conventional methods.

Synthesis of Low-Cost, High-Density DNA Microarrays

UW-Madison researchers have developed a system and method for synthesizing DNA microarrays using a device that includes a reduction optics assembly and a target assembly. These new components incorporate image reduction and precision stage motion into the synthesis process, increasing the density of the DNA chip to 25 times the density of a traditional microarray while maintaining the cost per feature. As a result, the system offers a significant reduction in the cost of DNA microarrays by increasing the amount of information contained within the microarray while keeping the consumables necessary for the process constant when compared to similar technologies.

Light-Directed DNA Synthesis Using Inverse Capping for Error Reduction

UW-Madison researchers have developed a method of reducing errors in light-directed DNA synthesis by using inverted masks to disable sites where synthesis is not intended to occur. Before light-directed DNA synthesis occurs on a prepared microarray substrate, the substrate is exposed to light via an inverse mask pattern to deprotect inactive regions of the substrate where synthesis is not desired. The deprotected sites are then capped to permanently disable the inactive areas. This inverse capping prevents unwanted DNA synthesis in the inactive areas, resulting in “purer” DNA, even though such areas may be unintentionally exposed to light during DNA synthesis on the active areas of the substrate.

Protein-Acrylamide Copolymer Hydrogels for Measuring Protein Concentration and Activity

UW-Madison researchers have developed a method of specifically attaching proteins to glass surfaces via copolymerization with a polyacrylamide hydrogel. They also have developed techniques for using the arrays formed using this process to detect proteins and measure their concentrations, binding affinities and kinetics.

Their method uses a surface functionalized with an acrylic acid- or acrylamide-based hydrogel. Proteins are labeled with an acrylic moiety and then attached to the functionalized surface through copolymerization with the hydrogel. The attached protein is then available for use in a variety of assays.

Image Locking System for DNA Microarray Synthesis

UW–Madison researchers have developed an image locking system for DNA microarray synthesis that will stabilize or “lock” the image with respect to an image capture device such as a camera or microscope. The system includes the use of detection or reference marks. When a shift in image position is detected, a correction signal is sent to one of two mirrors, moving the image to correct for the change in image position.

Plasma-Enhanced Functionalization of Inorganic Oxide Surfaces

UW-Madison researchers have developed an efficient, two-step technique for covalently attaching epoxide functionalities to glass, silicon, quartz, and other inorganic surfaces. First, an oxide surface is exposed to a cold plasma to create hydroxyl functionalities on the surface. Next, these hydroxyl groups are reacted with epoxy group-containing molecules in the absence of plasma to form surface-bound spacer chains. Biomolecules can then be immobilized on the resulting functionalized surface by reacting the biomolecules with the spacer chains.

Plasma-Enhanced Functionalization of Carbon-Containing Substrates

UW-Madison researchers have developed an efficient, dry plasma technique for functionalizing surfaces that holds several advantages over traditional wet chemical approaches. The technique involves two steps. First, a carbon containing substrate is exposed to an inert plasma (e.g., argon or hydrogen) that generates reactive active sites, such as free radicals or ions, on the surface of the substrate. Next, the surface is exposed to volatile compounds in the absence of plasma. The compounds react with the active sites to produce surface-bound spacer chain molecules containing one or more functional groups. These functional groups, in turn, can react with molecules of DNA or protein.

Methods and Devices for Precisely Dispensing Microvolumes of Fluids

UW-Madison researchers have developed a microplotter device that can deposit spots or lines on the order of 5 micrometers in size for several applications, including biological microarrays and polymer-based circuits. The device consists of a nozzle for depositing fluid, which is connected to a positioning system that is controlled by customized software on a desktop computer. The nozzle, composed of a micropipette fastened to a piece of piezoelectric, deposits small features through ultrasonics.