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Various research groups have developed their own methods, each differing in their approach, but can be summarized into 3 main groups.
[[Image:Figure 1 NAPPA.png|thumb|600px|'''Figure 1: Schematic diagramDiagram of NAPPA''']]
====Nucleic acid programmable protein array (NAPPA)====
;Nucleic acid programmable protein array (NAPPA): NAPPA<ref name="Ramachandran, N. 2004">Ramachandran, N., E. Hainsworth, et al. (2004). "Self-assembling protein microarrays." Science 305(5680): 86–90.</ref> uses DNA template that has already been immobilized onto the same protein capture surface. The DNA template is [[biotinylation|biotinylated]] and is bound to [[avidin]] that is pre-coated onto the protein capture surface. Newly synthesized proteins which are tagged with GST are then immobilized next to the template DNA by binding to the adjacent polyclonal anti-GST capture antibody that is also pre-coated onto the capture surface (Figure 1). The main drawback of this method is the extra and tedious preparation steps at the beginning of the process: (1) the [[molecular cloning|cloning]] of [[cDNA]]s in an expression-ready [[expression vector|vector]]; and (2) the need to biotinylate the [[plasmid]] DNA but not to interfere with transcription. Moreover, the resulting protein array is not ‘pure’ because the proteins are co-localized with their DNA templates and capture antibodies.<ref name="O. Stoevesandt, 2008"/>
[[Image:Figure 2 PISA.png|thumb|600px|'''Figure 2: Schematic diagramDiagram of PISA''']]
====Protein ''in situ'' array (PISA)====
; Protein ''in situ'' array (PISA): Unlike NAPPA, PISA<ref>He, M. and M. J. Taussig (2001). "Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method)." Nucleic Acids Res 29(15): E73-3.</ref> completely bypasses DNA immobilization as the DNA template is added as a free molecule in the reaction mixture. In 2006, another group refined and miniaturized this method by using multiple spotting technique to spot the DNA template and cell-free transcription and translation mixture on a high-density protein microarray with up to 13,000 spots<ref>Angenendt, P., J. Kreutzberger, et al. (2006). "Generation of high density protein microarrays by cell-free in situ expression of unpurified PCR products." Mol Cell Proteomics 5(9): 1658–66.</ref> (Figure 2). This was made possible by the automated system used to accurately and sequentially supply the reagents for the transcription/translation reaction occurs in a small, sub-nanolitre droplet.
[[Image:Figure 3 puromycin2.png|thumb|600px|'''Figure 3: Schematic diagramDiagram of ''In situ'' puromycin-capture''']]
====''In situ'' puromycin-capture====
; ''In situ'' puromycin-capture: This method is an adaptation of [[mRNA display]] technology. [[PCR]] DNA is first transcribed to [[mRNA]], and a single-stranded DNA [[oligonucleotide]] modified with [[biotin]] and [[puromycin]] on each end is then hybridized to the 3’-end of the mRNA. The mRNAs are then arrayed on a slide and immobilized by the binding of biotin to [[streptavidin]] that is pre-coated on the slide. Cell extract is then dispensed on the slide for ''in situ'' translation to take place. When the ribosome reaches the hybridized oligonucleotide, it stalls and incorporates the puromycin molecule to the nascent [[polypeptide]] chain, thereby attaching the newly synthesized protein to the microarray via the DNA oligonucleotide<ref>Tao, S. C. and H. Zhu (2006). "Protein chip fabrication by capture of nascent polypeptides." Nat Biotechnol 24(10): 1253–4.</ref> (Figure 3). A pure protein array is obtained after the mRNA is digested with [[RNase]]. The protein spots generated by this method are very sharply defined and can be produced at a high density.
===Nano-well array format===
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