DNA microarrays products

In contrast to DNA microarrays, production of protein microarrays is an immense technological challenge. The first challenge derives fi om the limited availability of proteins for the fabrication of vast amounts of protein microarrays. Whereas for DNA with the polymerase chain reaction PCR), a routine method exists to enormously increase the number of DNA copies and automated processes are established for oligonucleotide synthesis, for proteins such methods are missing hence, proteins are produced in very small quantities. Furthermore, the biochemistry of proteins is orders of magnitude more complex than DNA biochemistry, so that the production of protein microarrays is much more difficult. 

Diehn M et al. Large-scale identification of secreted and membrane-associated gene products using DNA microarrays. Nature Genet 2000 25 58-62. 

The main advantage of this experimental design is that both samples are compared on a single DNA microarray, and therefore errors that are due to the use of multiple microarrays, such as variation in microarray production, hybridization, and washing, are minimized. Time and money considerations are another important advantage of this design. 

PCR products, corresponding to these clones, should be present at multiple sites on the DNA microarray. We routinely put at least 20 spots for each clone. 

Beier M., Hoheisel J.D., Production by quantitative photolithographic synthesis of individually quality checked DNA microarrays, Nucl Acid Res. 2000 28 el 1. 

Yergeau E, Lawrence JR, Waiser MJ et al (2010) Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays. Appl Environ Microbiol 76(16) 5432-5439... 

The proteomics field is currently wide open. Only a few protein microarray products have been commercialized. Unlike DNA microarrays that are commonly constructed on essentially two platforms (GeneChip or slide array) employing oligonucleotides or cDNA probes, the protein microarray appears on a variety of platforms and with different types of probes. 

Other extensions that have been made include the construction of a biochip in which a reverse transcription PCRprocess can be carried out [384] and the integration of PCR with capillary electrophoresis [385], DNA microarray hybridization [386] and sample preparation [387,388]. The speed of analysis, the ease of integrating different functions and the relative low costs of micro-PCR production are important advantages of the miniaturized PCR technique that suggest that this bioorganic microreactor device will be thoroughly implemented in many analytical labs. 

There are however difficulties in running multiplex PCR, and it is difficult to differentiate PCR products of approximately the same size in a multiplex PCR or PCR-RFLP gel. However DNA microarrays do not have these problems, and have been used to serotype pathogenic strains and proved to be rapid, reliable and sensitive. The approach involves the immobilization of numerous oligonucleotide DNA probes on a solid support to which fluorescence-labeled amplified target DNA is hybridized, and is a powerful tool for the detection of pathogens by virtue of high throughput, speed and sensitivity. 

Sindelar G, Wendisch VF (2007) Improving lysine production by Corynebacterium glutamicum through DNA microarray-based identification of novel target genes. Appl Microbiol Biotechnol 76 677-689... 

FOOTPRINT software tool (www.prodoric.de, [92]). Visualisation is achieved via ProdoNet [93]. Consequently, DNA microarray and proteomic experiments are the experimental validation for our proposals. Furthermore, integration of regulatory and metabolic networks is desired. The identification of limiting steps in protein production and the deduction of molecular optimisation strategies are the major goals in the future. 

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