Universal protein array

H. Ge, UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions. Nucl. Acids Res. 28, e3 (2000). 

Ge (2000) carefully designed a universal protein array (UFA) system based on the use of various transcription factors, their activators, and cofactors as probes. A total of 48 different, highly purified factors were used to create the UFA on nitrocellulose filters. Frotein-protein interactions of various binding affinities could be assessed using different ionic strength buffers (e.g., 100 mM KCl vs. 1000 mM KCl). The relative binding of radiolabeled ( T) GST-K-p52 proteins to various transcription factors was studied. 

Universal protein array urokinaselike plasminogen activator... 

C.A. Mirkin, J.-H. Lim, D.S. Ginger, J.-M. Nam, K.-B. Lee, L. Demers, and A. Ivanisevic, Peptide and protein arrays and direct-write lithographic printing of peptides and proteins, US Patent 7842344, assigned to Northwestern University (Evanston, IL), November 30, 2010. 

Without highly specific binding to proteins on the chip, thorough washing of the array may remove specific binders as well as non-specific binders. Protein bindings cannot offer a universal detection scheme like hybridization used in DNA arrays, which makes it difficult to discover enough probes for proteomics. 

Other early work includes that of Moody et al. (2001) who spotted anticytokine monoclonals onto the bottom of polystyrene microtiter plates (Max-isorp, Nalge Nunc) and measured cytokine levels in stimulated peripheral blood mononuclear cells. Finally, although not strictly a microarray, the microwell array system developed by Michael Snyder s group at Yale University to measure kinase activity is a simple and elegant approach (Zhu et al., 2000). The "protein chip" is comprised of microwells fabricated in a flexible elastomer of PDMS [poly(dimethylsiloxane)] substrate by a molding process. 

Two hundred and forty-eight serum samples provided from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital (Chicago, IlUnios) were analyzed on the same ProteinChip arrays using both a PBS-II and a Qq-TOF MS fitted with a SELDI interface. The proteomic patterns of the serum samples were acquired on the PBS-II TOF MS, immediately followed by their acquisition on the Qq-TOF MS. The key to this study is that the identical set of serum samples was analyzed on the exact same protein-chip surface, eliminating all experimental variability other than the use of two different instruments. 

Figure 4 Sensitive protein detection using the RCA (rolling circle amplification) immunoassay chip and solid-phase direct fluorescence detection. The chip is divided into 16 teflon wells, each containing an array of 256 antibodies as probes. When a protein, represented by the blue square, is captured by one of the probes, it can be recognized using a second, biotinylated antibody (red), which is subsequentiy detected by a tertiary universal antibody connected to a circular oligonucleotide. A strand-displacing DMA polymerase can use this circular template, generating a long concatemer containing many fluorescent labels.

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