Microarray spotted array

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... 

Since the microarray spot images have many different sizes and shapes and some of the spots may not be located at the central position, addressing is essential to find the centre of the spots. In order to ensure accuracy of the measurements, an automatic spot detector is used to calculate the spacing between rows and columns of spots, the overall position of the array in the image and the spot size so that coordinates can be assigned to each of the spots in the array. 

Moran Mirabal, J. Tan, C. Orth, R. Williams, E. Craighead, H. Lin, D., Controlling microarray spot morphology with polymer liftoff arrays, Anal. Chem. 2007, 79, 1109 1114... 

Other terms also relate to the anatomy of the microarray (Figure 1.4). The probes are immobilized on the substrate at discrete (x, y) locations or spatially addressable sites. The probe spots [measured in microns (diameters) for a circular spotted array or as a side of a square for an in situ array] are often referred to as features or elements of an array. Thus, an array containing 10,000 features would have 10,000 probes arranged as an array on a substrate. 

The primary substrate for spotted arrays is the glass slide. The salient physical and chemical features of a microarray slide are optical clarity (including... 

One important outcome of the Hessner et al. studies was development of a method useful for determining microarray spot quality (2003a and 2003b). One of the drawbacks to using microarrays has been how to address quality assurance and quality control (QA/QC) issues regarding the printed product prior to use. After an array is printed, how do you best determine spotting consistency from slide to slide or batch to batch ... 

Figure 6.19 ImmunoRCA antihuman microarray dose response for pnrified IgE. Signals from six microarray spots were averaged for each point and the background (no IgE) signal was subtracted. Inset Microarray scanner image of antihuman IgE array incubated with 1 ng/mL IgE. (From Schweitzer, B. et al., Proc. Natl. Acad. Sci. USA, 97, 10113-10119, 2000. With permission.)...

Finally, an understanding of the making of a microarray is fundamentally important to those interested in producing "spotted" arrays and properly using them. While complementary (cDNA) microarray fabricahon on glass slides has been well studied, we have less experience with the attachment of oligonucleotides and the preparation of protein arrays. Moreover, additional substrates and surface chemistries that may be better suited for printing proteins are now available. 

Nucleic acid arrays are used in the research labs at F. Hoffmann-La Roche in two varieties. One is represented by the commercially available high-density oUgonn-cleotide arrays in which the samples are synthesized in situ and covalently bonnd to the substrate (Affymetrix ). The other is the so-called custom spotted arrays in which the droplets that contain different molecules are deposited on the substrate. If the nucleic acid sequence is known, but not available on a commercial chip, oligonucleotides are synthesized and deposited, hi cases for which the sequence is not known, microarrays of cDNA fragments or plasmids are used. 

In functional protein microarrays, set of proteins of interest or an entire proteome is over expressed, purified and spotted in an addressable microarray surface. The most obvious target molecules that can effectively be used to investigate protein binding and therefore protein microarray analysis are monoclonal antibodies or IgG. However, unlike DNA microarrays, antibody arrays may pose some practical concerns ... 

The second type of enzyme application in microfluidics is protein interaction studies. In order to study interactions between enzymes and substrates, peptides, or other proteins, an alternative to microtiter plates is the microarray. These arrays are very often used in conjunction with microfluidic sample and reagent delivery systems alternatively, microchannels can be used to deposit spots in an array. By immobilizing substrates or inhibitors on the array, it is possible to screen large numbers of molecules for their relative abilities to bind a particular enzyme. This is typically accomplished by tagging the enzyme with a fluorescent molecule and using the intensity of the array spots to determine the amount of enzyme bound (Fig. 3a). This is a promising... 

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