Genome-Wide Analyses of mRNA and Proteins

Owing to the increasing availability of complete genome sequences, the analysis of transcription by DNA microarrays has managed to achieve an almost genomic scale measurement of mRNA levels. DNA microarrays were initially developed to quantify relative gene expression at the transcriptional level, that is, mRNA. The approach has then been extended to the analysis of single nucleotide polymorphisms (SNP) in DNA 

Essentially two fabrication approaches exist, leading to microarrays with different properties. In one approach, customized cDNA probes are prepared separately and then mechanically spotted on the support, with a density of about 10,000 spots/cm [52,53]. Because of errors in the handling and printing of probes, this procedure is prone to erroneous arraying [54]. The second approach uses photolithographic techniques to carry out the parallel synthesis of the oligonucleotides directly on the surface [55,56]. The length of the probes is typically for only 14 to 25 bases, much shorter than for 

Cross-hybridization hinders precise measurement of mRNAs, especially for rare sequences [61,62]. Also with an optimized probe set that is designed to minimize unspecific hybridization, the typical incubation time of about 12 h dedicated to hybridization does not allow low abundance targets to reach thermodynamic equilibrium, and their concentration is overestimated [61]. It follows that DNA arrays are also not suited for directly measuring expression levels in single cells, perhaps with the exception of enormously sized cells such as oocytes. This intrinsic limitation is obviated by first amplifying the RNA, although some of the ratios between mRNA may change in this additional step [63]. 

Protein function is a direct consequence of its amino acid sequence. Further, protein activity depends on proper folding, post-translational modifications, and interactions 

In analogy to DNA arrays, protein microarrays are under development. These devices should enable investigators to quantify expression levels, discover bimolecular interactions, assign functions, and perform structural studies [82,83]. Thus far, only the potential of protein arrays has been validated in pilot studies. Before robust and flexible analytical 

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