Protein Microarray - Making The Array

Making The Array

The proteins are arrayed onto a solid surface such as microscope slides, membranes, beads or microtitre plates. The function of this surface is to provide a support onto which proteins can be immobilized. It should demonstrate maximal binding properties, whilst maintaining the protein in its native conformation so that its binding ability is retained. Microscope slides made of glass or silicon are a popular choice since they are compatible with the easily obtained robotic arrayers and laser scanners that have been developed for DNA microarray technology.

The chosen solid surface is then covered with a coating that must serve the simultaneous functions of immobilising the protein, preventing its denaturation, orienting it in the appropriate direction so that its binding sites are accessible, and providing a hydrophilic environment in which the binding reaction can occur. In addition, it also needs to display minimal non-specific binding in order to minimize background noise in the detection systems. Furthermore, it needs to be compatible with different detection systems. Immobilising agents include layers of aluminium or gold, hydrophilic polymers, and polyacrylamide gels, or treatment with amines, aldehyde or epoxy. Thin-film technologies like physical vapour deposition (PVD) and chemical vapour deposition (CVD) are employed to apply the coating to the support surface.

An aqueous environment is essential at all stages of array manufacture and operation to prevent protein denaturation. Therefore sample buffers contain a high percent of glycerol(to increase the freezing point), and the humidity of the manufacturing environment is carefully regulated. Microwells have the dual advantage of providing an aqueous environment while preventing cross-contamination between samples.

In the most common type of protein array, robots place large numbers of proteins or their ligands onto a coated solid support in a pre-defined pattern. This is known as robotic contact printing or robotic spotting. Another fabrication method is ink-jetting, a drop-on-demand, non-contact method of dispersing the protein polymers onto the solid surface in the desired pattern. Piezoelectric spotting is a similar method to ink-jet printing. The printhead moves across the array, and at each spot uses electric stimulation to deliver the protein molecules onto the surface via tiny jets. This is also a non-contact process. Photolithography is a fourth method of arraying the proteins onto the surface. Light is used in association with photomasks, opaque plates with holes or transparencies that allow light to shine through in a defined pattern. A series of chemical treatments then enables deposition of the protein in the desired pattern upon the material underneath the photomask.

The capture molecules arrayed on the solid surface may be antibodies, antigens, aptamers (nucleic acid-based ligands), affibodies (small molecules engineered to mimic monoclonal antibodies), or full length proteins. Sources of such proteins include cell-based expression systems for recombinant proteins, purification from natural sources, production in vitro by cell-free translation systems, and synthetic methods for peptides. Many of these methods can be automated for high throughput production but care must be taken to avoid conditions of synthesis or extraction that result in a denatured protein which, since it no longer recognizes its binding partner, renders the array useless.

Proteins are highly sensitive to changes in their microenvironment. This presents a challenge in maintaining protein arrays in a stable condition over extended periods of time. In situ methods involve on-chip synthesis of proteins as and when required, directly from the DNA using cell-free protein expression systems. Since DNA is a highly stable molecule it does not deteriorate over time and is therefore suited to long-term storage. This approach is also advantageous in that it circumvents the laborious and often costly processes of separate protein purification and DNA cloning, since proteins are made and immobilised simultaneously in a single step on the chip surface. Examples of In situ techniques are PISA (protein in situ array), NAPPA (nucleic acid programmable protein array) and DAPA (DNA array to protein array).