Microarray DNA Hybridization

Barker CS, Griffin C, Dolganov GM et al. Increased DNA microarray hybridization specificity using sscDNA targets. BMC Genomics 2005 6 57. 

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. 

Spike-ins are usually RNA transcripts used to calibrate measurements in a DNA microarray experiment. Each spike-in is designed to hybridize with a specific control probe on the target array. Manufacturers of commercially available microarrays typically offer companion RNA spike-ins kits . Known amounts of RNA spike-ins are mixed with the experiment sample during preparation. Subsequently the measured degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA. 

Shalon, D., Smith, S. J., and Brown, P. O. (1996). A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639-645. 

Oxford Gene Technologies offers services and licenses their proprietary technologies. The array technique surveys hybridization across gene sequences. The customized DNA microarray service supports research activities, and includes consultation, experimental design, data analysis, and interpretation. 

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. 

In an indirect comparison design, the free and polysome samples are labeled with a red fluorescent dye, and each is hybridized independently to a DNA microarray against an RNA sample that is labeled with green fluorescent dye (Fig. 10.IB). Because the green-labeled sample is the same for both samples, it serves as a common reference and the polysome-to-free ratio can... 

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. 

A similar type of biotin-dendritic multimer also was used to boost sensitivity in DNA microarray detection by 100-fold over that obtainable using traditional avidin-biotin reagent systems (Stears, 2000 Striebel et al., 2004). With this system, a polyvalent biotin dendrimer is able to bind many labeled avidin or streptavidin molecules, which may carry enzymes or fluorescent probes for assay detection. In addition, if the biotinylated dendrimer and the streptavidin detection agent is added at the same time, then at the site of a captured analyte, the biotin-dendrimer conjugates can form huge multi-dendrimer complexes wherein avidin or streptavidin detection reagents bridge between more than one dendrimer. Thus, the use of multivalent biotin-dendrimers can become universal enhancers of DNA hybridization assays or immunoassay procedures. 

Y. Belosludtsev, B. Iverson, S. Lemeshko, R. Eggers, R. Wiese, S. Lee, T. Powdrill, and M. Hogan, DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Anal. Biochem. 292, 250—256 (2001). 

Immunoaffinity chromatography (IAC), 6 400—402 12 137, 145 Immunoanalyzers, automated, 14 150 Immunoassay(s), 14 135-159. See also Immunoassay- DNA probe hybrid assays Immunoassay methods Immuno(bio)sensors antibody-antigen reaction, 14 136-138 basic technology in, 14 138-140 chemiluminescent, 14 150-151 classification of, 14 140-153 design of, 14 139-140 enzyme, 14 143-148 fluorescence, 14 148-150 highly specific, 14 153 historical perspective on, 14 136 microarrays and, 14 156—157 microfluidics in, 26 968—969 monoclonal versus polyclonal antibodies in, 14 152-153... 

Lein ES, Zhao X, Gage EH. 2004. Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization. J Neurosci 24 ... 

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