MAGIChips, also known as "microarrays of gel-immobilized compounds on a chip" or "three-dimensional DNA microarrays", are devices for molecular hybridization produced by immobilizing oligonucleotides, DNA, enzymes, antibodies, and other compounds on a photopolymerized micromatrix of polyacrylamide gel pads of 100x100x20 μm or smaller size. This technology is used for analysis of nucleic acid hybridization, specific binding of DNA, and low-molecular weight compounds with proteins, and protein-protein interactions. The gel pads increase the surface for hybridization to 50 times, compared to typical microarrays which are printed on flat surface of a glass slide that is usually treated by chemical compounds on which the probes adhere. A probe density of more than 1012 molecules per gel pad can be achieved due to 3D nature of the gel pads. The array is based on a glass surface that has small polyacrylamide gel units affixed to it. Each gel unit functions as an individual reaction cell as it is surrounded by a hydrophobic glass surface that prevents mixing of the solution in the gel units. This lays a foundation for performing ligation, single base extension, PCR amplification of DNA, on-chip MALDI-TOF mass spectrometry and other reactions.
Historical background MAGIChip technology was developed as a result of collaboration between Dr. David Stahl at University of Washington and Dr Andrei Mirzabekov, formerly of Argonne National laboratory. Andrei Mirzabekov initiated the development of the DNA sequencing by hybridization with oligonucleotides: a novel method in 1988. This method was a foundation for the biotechnology that uses biological microchips to identify DNA structures rapidly, which is of great importance in the fight against a variety of diseases. A joint research project was announced in 1998 among Motorola Inc, Packard Instrument Company and the U.S. Department of Energy's Argonne National Laboratory. In 1999, the researchers at Argonne National Lab pushed the development of microarray-type biochip technology they co-designed with the Engelhardt Institute to ward off a worldwide outbreak of tuberculosis. Motorola developed manufacturing processes to mass-produce biochips, and Packard developed and manufactured the analytical instruments to process and analyze the biochips. Argonne's contribution, in conjunction with Engelhardt Institute of Molecular Biology (EIMB), was intellectual property in the form of 19 inventions related to biological microchips. But this collaboration between EIMB in Moscow and Argonne National Laboratory at Illinois and two other US-based commercial partners collapsed as result of argument on contractual arrangement between the parties in 2001. As a result of this dispute, Dr Andrei Mirzabekov resigned as a director of Argonne's Biochip Technology Centre.
Method Arrays of gel elements (pads) are created on the glass surface (micromatrix) which is followed by application and chemical immobilization of different compounds (probes) onto these gel pads. Test sample is then added to this micromatrix containing immobilized probes in gel pads and molecular recognition reactions are allowed to take place under specified conditions. The test sample is fluorescent labelled to monitor the molecular interactions. The analysis of molecular interaction patterns is done by using specialized software.
The array of gel elements on a glass slide is prepared by ‘’’photopolymerization‘’’. The acrylamide solution to be polymerized is applied to the polymerization chamber. Polymerization chamber consists of a quartz mask, two Teflon spacers, and a microscopic glass slide, clamped together by two metal clamps. The inner side of quartz mask has ultraviolet (UV)-transparent windows arranged in a specified spatial manner in a non-transparent chromium film. Assembled chamber containing the acrylamide gel is exposed to UV light to allow polymerization in only those positions of the chamber that are situated directly under the transparent windows. Oligonucleotides or DNA fragments need to be activated to contain chemically reactive groups to facilitate coupling with the activated gel elements. Probe activation depends on the chemistry of activation of the polyacrylamide gels. Thus to immobilize in the aldehyde-containing gel the probe should have reactive amino group and if the gels are activated by introduction of amino groups, the probes should contain free aldehyde group. Probes are usually prepared by introduction of chemically active groups in terminal position of the oligonucleotides during their synthesis. Probes for immobilization are transferred into gel elements of micromatrix by using dispensing robots. The fibre-optic pin of the robots has a hydrophobic side surface and a hydrophilic tip, and operates at a dew temperature to prevent evaporation of the sample during transfer. The activated probes are chemically immobilized by coupling oligonucleotides bearing amino or aldehyde groups with gel supports containing aldehyde or amino groups respectively. The target molecules are labelled with fluorescent dyes. The fluorescent detection enables monitoring the process in real time with high spatial resolution. The criteria for labelling procedure includes –
It should be simple, fast and inexpensive It should be applicable to both RNA and DNA targets It should be compatible with fragmentation required to decrease secondary structure formation It should allow incorporation of one label into one fragment to ensure proper quantification of the hybridization intensity It should allow coupling of multiple dyes
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