Microarray targets attachment

The origin of the microarray or biochip can be traced to a seminal publication by Edwin Southern over 30 years ago. Southern described a method by which DNA could be attached to a solid support following electrophoresis and interrogated for sequences of interest by hybridization with a complementary DNA sequence (16). The complementary DNA sequence, termed a probe, was labeled with either a radioactive or a fluorescent marker and hybridized to the DNA target sample, which was immobilized on a sohd support, such as a nitrocellulose filter membrane. 

Electronically active chips (e.g.. Nanogen s NanoChip Electronic Microarray) are true microchips in which microelectrodes (pads) become elements of the array (Figure 2.13). The microelectrodes are covered with materials that allow immobilization of probes. Each electrode is individually addressable so that specific probes can be attached to different electrodes. Hybridization is accelerated by electromotive force (emf) on the target. Enhanced stringency is also achieved by modulation of the emf (Heller et al., 2000). 

The best substrate will present the probe to the soluhon phase with as much rotahonal freedom as possible so that it can undergo favorable binding with the incoming target molecule. The binding should approximate free solution association. Table 3.2 lists common coupling chemistries employed for probe (nucleic acid and protein) attachments useful for microarrays. 

The basic elements required for the DNA microarray are the solid substrate, the attachment chemistry of the probe to the solid support, the approach adopted to spot the probes at particular locations of the two-dimensional array, the method employed to bring the solution target to the appropriate location of the array (passive or active), and the readout modality. A brief discussion of some of these important elements is given in Sects. 3.2.1-3.2.3. 

With some detection technologies compounds can be screened in microarrays instead of plate wells. This requires that either the small molecule or the target be attached to a solid support, usually a glass slide, as shown in Figure 6.9. The other potential binding partner, which can be labeled (say with a fluorescent dye if fluorescence microscopy is used) or unlabeled (if surface plasmon resonance detection, discussed later, is to be used), is then exposed to the shde and interactions are detected. 

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