The sequencing of entire genomes has made it possible to examine the level of gene expression in a particular cell or tissue by using oligonucleotide probes to assess the level of mRNA from a particular gene. This is done most effectively through the use of
A. Screening of genome libraries
B. DNA microarrays
C. Gene disruption or knockout
D. ELISA

Examining Gene Expression Using DNA Microarrays

The sequencing of entire genomes has revolutionized the study of gene expression and functional genomics. Understanding gene expression levels in a particular cell or tissue provides insights into cellular functions, disease mechanisms, and drug responses. Among various available techniques, DNA microarrays have emerged as one of the most effective tools for assessing the level of mRNA from a specific gene using oligonucleotide probes.

Correct Answer:

The correct answer is B. DNA microarrays.

Why DNA Microarrays Are the Best Tool for Gene Expression Analysis

1. High-Throughput Gene Expression Analysis

• DNA microarrays allow the simultaneous measurement of the expression levels of thousands of genes.
• It involves hybridizing fluorescently labeled cDNA (complementary DNA) to probes on a solid surface (glass slide or chip).

2. Specificity and Sensitivity

• Oligonucleotide probes are designed to match specific gene sequences.
• Only perfectly matched sequences hybridize, ensuring accurate detection of gene expression levels.

3. Quantitative Analysis

• The intensity of the fluorescence signal reflects the abundance of mRNA from a particular gene.
• This enables both quantitative and qualitative assessment of gene expression.

4. Comparative Gene Expression Studies

• DNA microarrays are used to compare gene expression between different samples:
  • Healthy vs. diseased tissue
  • Treated vs. untreated cells
  • Time-course studies of gene expression

How DNA Microarrays Work

1. Preparation of Sample and Probes

• mRNA is extracted from the cell or tissue sample.
• mRNA is reverse-transcribed into cDNA using fluorescently labeled nucleotides.

2. Hybridization

• The labeled cDNA is incubated with the DNA microarray slide.
• Each spot on the slide contains oligonucleotide probes complementary to specific genes.
• If the cDNA matches the probe, hybridization occurs.

3. Detection

• The slide is scanned using a laser to detect the fluorescence signal.
• The intensity of the signal corresponds to the level of gene expression.

4. Data Analysis

• The fluorescence intensity is analyzed using bioinformatics tools.
• This generates a heatmap or expression profile of the analyzed genes.

Why Other Options Are Incorrect

Advantages of DNA Microarrays for Gene Expression

1. High-Throughput:

• Thousands of genes can be analyzed simultaneously.

2. Specific and Accurate:

• Oligonucleotide probes ensure high specificity.

3. Quantitative:

• Fluorescence intensity reflects the precise level of gene expression.

4. Comparative Studies:

• Useful for comparing gene expression across different experimental conditions.

Challenges with DNA Microarrays

1. Cross-Hybridization:

• Non-specific binding can reduce accuracy.

2. Sensitivity Limitations:

• Low-abundance mRNA may not be detected.

3. Cost:

• High costs for microarray chips and analysis tools.

Applications of DNA Microarrays in Research and Medicine

1. Cancer Research:

• Identifying differentially expressed genes in tumors.

2. Drug Discovery:

• Studying drug effects on gene expression.

3. Disease Diagnosis:

• Identifying gene expression patterns in diseases like diabetes and neurodegenerative disorders.

4. Developmental Biology:

• Studying gene expression changes during embryonic development.

Example of DNA Microarray Experiment

1. A researcher extracts mRNA from normal and cancerous tissue.
2. The mRNA is converted to cDNA using fluorescent dyes:
   • Green dye for normal tissue
   • Red dye for cancerous tissue
3. The cDNA is hybridized to a DNA microarray slide.
4. After washing, the slide is scanned:
   • Green = Higher expression in normal tissue
   • Red = Higher expression in cancer tissue
   • Yellow = Equal expression in both tissues

Why DNA Microarrays Are Effective for Gene Expression

• DNA microarrays provide a global view of gene expression.
• They are highly specific and quantitative.
• The ability to analyze thousands of genes simultaneously makes them invaluable for molecular biology research.

Conclusion

DNA microarrays are the most effective method for assessing gene expression from oligonucleotide probes. Their ability to provide quantitative, specific, and high-throughput analysis makes them an essential tool in molecular biology and biomedical research. While other methods like gene knockout and ELISA serve different purposes, DNA microarrays remain the gold standard for analyzing gene expression at a large scale.