Microarrays are lab-on-chip devices which allow scientists to investigate the expression of thousands of genes in multiple samples simultaneously. The chip is mainly composed of glass, silicon or plastics. On the surface of chip thousands of spots are arrayed, and each spot contains multiple copies of DNA sequences which correspond to a particular gene. One of the applications of microarrays is to allow us to compare expression of various genes in different samples, making microarrays a powerful tool in Detection techniques and life science research.
Applications of microarrays
Tumor formation involves changes of numerous genes, and a DNA (cDNA) microarray can provide a platform which allows medical scientists to have a better understanding of gene expression in different clinical samples. Some types of cancer such as breast cancer are highly heterogeneous containing various molecular and clinical subtypes.
Different clinical subtypes of cancer can show different prognosis to the same treatment due to variation in gene expression. However, exactly how cancer heterogeneity affects prognosis and treatment response of patients has yet to be fully understood. Nonetheless, DNA microarray technologies provide medical scientists an opportunity to analyze and compare expression profile of different cancer clinical/molecular subtypes. By comparing gene expression profiles between samples from different cancer subtypes and normal tissues using microarray technologies, scientists can identify specific genes that are expressed/silenced in each molecular subtype of cancer and scientists can understand how particular genes affect treatment response. Ultimately, scientists can use this technology to identify putative drug targets for cancer treatment.
How to perform a DNA microarray analysis
Multiple preparation steps are required to perform a successful DNA microarray for comparing genes expression in different samples.
Firstly, mRNA must be purified from both experimental sample (e.g., cancer cells) and referee sample (e.g., normal healthy cells) by using an organic solvent. Secondly, mRNA from experimental and referee sample are converted to complementary DNA (cDNA) by reverse transcriptase, and fluorescent probes of different colors are used to label the cDNA samples.
The color of fluorescent probes used in experimental and referee samples should be different (e.g., green fluorescent for referee sample and red fluorescent for experimental sample). Afterward, cDNA from the two samples (from cancer and healthy cells) are added onto the microarray chip. cDNA from the samples hybridize to the complementary strand on the microarray so that each spot on the microarray contains a specific nucleotide sequence which represents a particular gene. The microarray will then be washed to wash off excess cDNA that did not hybridize to the complementary strand. Finally, the microarray will be analyzed in a scanner (exposed to laser) to examine fluorescent of every single spot for red and green. The results of red and green fluorescent will be merged.
What does the result of DNA microarray means?
The fluorescence intensity is positively correlated to the amount of cDNA from each sample. The appearance of red fluorescence in a spot means the gene is highly expressed in experimental sample (e.g., tumor cells) while the appearance of green fluorescence in a spot means the gene is actively expressed in referee sample (healthy cells). For a gene that is highly expressed in both the experimental and referee samples, the spot will be yellow in color when exposed to the laser.
One of the limitations of DNA microarrays is that expression of mRNA is not fully correlated to protein expression profile of organisms. Therefore, protein microarrays have been developed to examine and compare protein expression profiles of different samples. The principle of DNA and protein microarrays is similar, but antibodies are used to capture/hybridize with target proteins in protein microarray.
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