Tissue microarrays as a platform for proteomic investigation
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Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018-2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.
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Protein microarray analysis has had a major impact in modern biology and medicine by enabling detection of hundreds of proteins (and other molecules) using extremely small sample volumes [1-4]. Protein microarrays are printed on a glass slide using a robot and are only a few millimeters in diameter. Each consists of a grid of several hundred spots (100-200μm-diameter) of protein. Protein microarrays can be divided into two categories: target protein arrays [5] and antibody (Ab) microarrays [6]. Target protein microarrays have been used to study protein interactions with pharmaceutical drugs [7], enzyme substrates [8] and antibodies [9, 10]; the latter are examples of “antigen (Ag) microarrays”. Ab microarrays are arrays printed with antibodies, each of which binds to and recognizes a specific molecule termed the “antigen”. Some antibodies printed in a microarray format can detect antigens at concentrations below 1ng/ml [6]. Used most extensively for the analysis of human proteins in biomedical applications [11-15], this type of array has not been used for the detection of microbial or viral antigens in environmental samples [although microbial/viral antigen microarrays have been used for serodiagnosis [16]]. We have proposed that such a microbe-specific Ab microarray would provide a useful tool for in situ detection of biological molecules in space (due to its low mass, broad search capability and small sample required).
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Large genomes contain families of highly similar genes that cannot be individually identified by microarray probes. This limitation is due to thermodynamic restrictions and cannot be resolved by any computational method. Since gene annotations are updated more frequently than microarrays, another common issue facing microarray users is that existing microarrays must be routinely reanalyzed to determine probes that are still useful with respect to the updated annotations. PICKY 2.0 can design shared probes for sets of genes that cannot be individually identified using unique probes. PICKY 2.0 uses novel algorithms to track sharable regions among genes and to strictly distinguish them from other highly similar but nontarget regions during thermodynamic comparisons. Therefore, PICKY does not sacrifice the quality of shared probes when choosing them. The latest PICKY 2.1 includes the new capability to reanalyze existing microarray probes against updated gene sets to determine probes that are still valid to use. In addition, more precise nonlinear salt effect estimates and other improvements are added, making PICKY 2.1 more versatile to microarray users. Shared probes allow expressed gene family members to be detected; this capability is generally more desirable than not knowing anything about these genes. Shared probes also enable the design of cross-genome microarrays, which facilitate multiple species identification in environmental samples. The new nonlinear salt effect calculation significantly increases the precision of probes at a lower buffer salt concentration, and the probe reanalysis function improves existing microarray result interpretations.
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Microarrays play an increasingly significant role in drug discovery. Written by a leader in the field, Applying Genomic and Proteomic Microarray Technology in Drug Discovery highlights, describes, and evaluates current scientific research using microarray technology in genomic and proteomic applications. The author addresses the drawbacks, helping
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Traditional protein microarrays require time-consuming processes of protein production and purification since the protein activities are not stable and the array products could not be stored properly for a long time.Self-assembling protein microarrays utilized cell-free expression system and DNA immobilization technique,which allowed multiple-protein expression simultaneously and in situ immobilization on the surface of arrays.This technology effectively overcomes the problems of traditional protein microarrays,and provides a useful tool for functional proteomics analysis.Currently,self-assembling protein microarrays are primarily used for screening protein-protein interactions,identifying immunodominant antigens and so on.This review focused on the recent advancement and application research on self-assembling protein microarrays.
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