Spotted DNA microarrays

Genome-Wide Analysis of mRNA Polysomal Profiles with Spotted DNA Microarrays... 

Townsend JP. 2003. Multifactorial experimental design and the transactivity of ratios with spotted DNA microarrays. 

Spotted DNA microarrays were the first to enter the market in the mid-1990s (6) and, in spite of improvements and competitors, they have continued in use today. The name of this type of arrays comes from the fact that the probes, which are the sequences on the array that will act as templates for the sequences from the sample target molecules, are first synthesized and then printed, or spotted on a glass slide (13). Sequences for the probes are... 

There are many protocols and different types of platforms available, e.g. GeneChips from Affymetrix, Illumina Bead Arrays, Arrays from Agilent, Applied Biosystems, GE Healthcare, customized spotted cDNA microarrays etc. the basic procedure for a large-scale measurement of gene expression involves the preparation of total or mRNA from the biological sample(s) under investigation (e.g. candidate tissue) and the hybridization of copied labelled RNA or cDNA to the DNA elements on the array surface (Fig. 1). 

It should be possible to extend the DNA microarray-binding experiment to whole-genome analysis of transcription factor binding sites. The authors suggest that a microarray spotted with 12,000 one-kilobase sequences would span the entire Saccharomyces cerevisiae genome (Bulyk et al., 2001). Such an array could be used to characterize the sequence specificity of S. cerevisiae transcription factors. These experiments would be useful for predicting functions of previously uncharacterized transcription... 

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. 

Currently, most commercially available DNA microarrays include spots that correspond to in vitro transcribed RNA from an unrelated organism (Yang, 2006). These RNAs can be either purchased as a ready-to-use mix or synthesized in vitro. 

The DNA microarrays are spotted on glass slides coated with amino-silane (Coming GAPS II). They should be ready for hybridization immediately when the labeled cDNA is ready. Thus, while the dyes are couplingto the cDNA (step 3 in the previous section), it is recommended to start the following process. 

The advent of the polymerase chain reaction (PCR) made it possible to directly spot down cDNA amplicons onto membranes, giving rise to the Southern dot blot format. In fact, the dot blot should be regarded as one of the earliest, if not the first, array format (albeit a macroarray). Why did many abandon the membrane in favor of the glass substrate for DNA microarrays ... 

Diehl, R, Grahlmann, S., Beier, M., and Hoheisel, J.D., Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acid Res., 29(7), 1-5, 2001. 

The characterisation of memory-related genes and proteins belongs to the hot spots of current memory research (D Agata and Cavallaro 2002). Respective studies in the field of aversive memories employ different molecular biological methods including in situ hybridisation (Ressler et al. 2002), differential display (Huang et al. 1998), subtractive hybridisation (Stork et al. 2001) and DNA microarrays (Kida et al. 2002). Most critical for the correct interpretation... 

Probe cDNA which is 500 5,000 bases long, is immobilized onto a solid surface such as glass using robot spotting. Then, it is exposed to a set of probes either separately or in a mixture. This method was developed at Stanford University and is called conventional DNA microarray. ... 

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