DNA Microarray (DNA chip) technique

Summary

DNA microarrays, or DNA chips, are powerful tools used for gene expression analysis and genotyping. The process begins with extracting RNA from samples, converting it into cDNA, and labeling it with fluorescent colors. The cDNA is then applied to a microarray, where probes corresponding to specific genes allow us to observe gene expression. By scanning the array, we can identify which genes are active in different tissue samples, such as healthy versus tumor tissue. This technology aids in understanding gene behavior, disease diagnosis, and developing personalized treatments.

Takeaways

• 😀 DNA microarrays, also known as DNA chips, are used for gene expression analysis and genotyping.
• 😀 The first step in microarray analysis is sample preparation, where RNA is extracted from tissues and transcribed into cDNA.
• 😀 cDNA from healthy tissue is labeled with a green fluorescent dye, while cDNA from tumor tissue is labeled with a red dye.
• 😀 Each spot on a microarray contains probes that are complementary to specific gene sequences.
• 😀 If cDNA from a sample hybridizes with the probes on a spot, the spot will light up in the color corresponding to the sample's fluorescent label.
• 😀 In the case of gene X, if the spot appears green, it means gene X is expressed in the healthy sample but not in the tumor sample.
• 😀 If gene Y's spot appears red, it indicates gene Y is expressed in the tumor sample but not in the healthy sample.
• 😀 If a spot turns yellow, it suggests that both samples express the gene, as both the green and red fluorescent dyes are present.
• 😀 Microarray analysis involves adding the cDNA samples to the entire chip, which is then scanned with a laser to detect fluorescence.
• 😀 The raw data from the laser scan is analyzed using bioinformatics to understand gene expression patterns in the samples.

Q & A

What is the purpose of a DNA microarray?

A DNA microarray, also known as a DNA chip, is a tool used for gene expression analysis and genotyping. It helps in determining which genes are active or expressed in a given sample.

How are samples prepared for DNA microarray analysis?

Sample preparation involves extracting RNA from the samples, such as healthy tissue (sample 1) and tumor tissue (sample 2). The RNA is then transcribed into complementary DNA (cDNA) using reverse transcription, and the cDNA is fluorescently labeled—green for healthy tissue and red for tumor tissue.

What role does fluorescence play in DNA microarray analysis?

Fluorescence is used to distinguish between different samples. cDNA from healthy tissue is labeled green, while cDNA from tumor tissue is labeled red. The fluorescent signals help identify gene expression in each sample after hybridization with specific probes on the microarray.

How does a DNA microarray detect gene expression?

In the DNA microarray, each spot contains probes that bind to specific genes. When the fluorescently labeled cDNA samples are added, the probes hybridize with complementary cDNA molecules. After washing, the spots are scanned with a laser, and the resulting fluorescence indicates whether the gene is expressed in the sample.

What does it mean if a spot appears green on the microarray?

A green spot on the microarray indicates that the gene is expressed in the healthy sample (sample 1) but not in the tumor sample (sample 2). This is because the green cDNA from the healthy tissue hybridizes with the probes for that gene.

What does a red spot on the microarray indicate?

A red spot indicates that the gene is expressed in the tumor tissue (sample 2) but not in the healthy tissue (sample 1). The red cDNA from the tumor sample hybridizes with the gene-specific probes.

What does a yellow spot signify in the DNA microarray?

A yellow spot means that both the healthy and tumor samples contain cDNA that can hybridize with the gene-specific probes. This suggests that the gene is expressed in both the healthy and tumor tissues.

What happens during the hybridization process in a DNA microarray?

During hybridization, cDNA from both the healthy and tumor samples is introduced to the microarray. The cDNA molecules bind (hybridize) to complementary probes on the array, which are short oligonucleotides that represent specific genes.

How is the fluorescence measured after hybridization?

A laser excites the fluorescent dye attached to the cDNA. The emitted fluorescence is then detected by a scanner, and the intensity of the signals from each spot is measured to determine the expression levels of the corresponding genes.

What is the role of bioinformatics in DNA microarray analysis?

Bioinformatics is used to analyze the raw data generated from the DNA microarray scan. This analysis helps in interpreting the fluorescence intensities and drawing conclusions about gene expression in the samples.