DNA Microarray- Definition, Principle, Procedure, Types

DNA microarrays are solid supports, usually of glass or silicon, upon which DNA is attached in an
organized, pre-determined grid fashion.
Each spot of DNA, called a probe, represents a single gene.
DNA microarrays can analyze the expression of tens of thousands of genes simultaneously.
There are several synonyms for DNA microarrays, such as DNA chips, gene chips, DNA arrays,
gene arrays, and biochips.

Types of DNA Microarrays

There are 2 types of DNA Chips/Microarrays:
1. cDNA based microarray
2. Oligonucleotide based microarray
Spotted DNA arrays (“cDNA arrays”)
 Chips are prepared by using cDNA.
 Called cDNA chips or cDNA microarray or probe DNA.
 The cDNAs are amplified by using PCR.
 Then these immobilized on a solid support made up of nylon filtre of glass slide (1 x 3 inches).
The probe DNA are loaded into a spotting spin by capillary action.
 Small volume of this DNA preparation is spotted on solid surface making physical contact
between these two.
 DNA is delivered mechanically or in a robotic manner.
Oligonucleotide arrays (Gene Chips)
 In oligonucleotide microarrays, short DNA oligonucleotides are spotted onto the array.
 Small number of 20-25mers/gene.
  The main feature of oligonucleotide microarray is that each gene is normally represented by
more than one probe.
 Enabled by photolithography from the computer industry
Requirements of DNA Microarray Technique
There are certain requirements for designing a DNA microarray system, viz:
1. DNA Chip
2. Target sample (Fluorescently labelled)
3. Fluorescent dyes
4. Probes
5. Scanner

Steps Involved in cDNA based Microarray

The reaction procedure of DNA microarray takes places in several steps:
1. Collection of samples
 The sample may be a cell/tissue of the organism that we wish to conduct the study on.
 Two types of samples are collected: healthy cells and infected cells, for comparison and to
obtain the results.
2. Isolation of mRNA
 RNA is extracted from the sample using a column or solvent like phenol-chloroform.
 From the extracted RNA, mRNA is separated leaving behind rRNA and tRNA.
 As mRNA has a poly-A tail, column beads with poly-T-tails are used to bind mRNA.
 After the extraction, the column is rinsed with buffer to isolate mRNA from the beads.
3. Creation of labeled cDNA
 To create cDNA (complementary DNA strand), reverse transcription of the mRNA is done.
 Both the samples are then incorporated with different fluorescent dyes for producing
fluorescent cDNA strands. This helps in distinguishing the sample category of the cDNAs.
4. Hybridization
 The labeled cDNAs from both the samples are placed in the DNA microarray so that each cDNA
gets hybridized to its complementary strand; they are also thoroughly washed to remove
unbounded sequences.
5. Collection and analysis
 The collection of data is done by using a microarray scanner.
 This scanner consists of a laser, a computer, and a camera. The laser excites fluorescence of
the cDNA, generating signals.
 When the laser scans the array, the camera records the images produced.
 Then the computer stores the data and provides the results immediately. The data thus
produced are then analyzed.
 The difference in the intensity of the colors for each spot determines the character of the gene
in that particular spot.
Applications of DNA Microarray
In humans, they can be used to determine how particular diseases affect the pattern of gene
expression (the expression profile) in various tissues, or the identity (from the expression
profile) of the infecting organism. Thus, in clinical medicine alone, DNA microarrays have huge
potential for diagnosis.
Besides, it has applications in many fields such as:
 Discovery of drugs
 Diagnostics and genetic engineering
 Alternative splicing detection
 Proteomics
 Functional genomics
 DNA sequencing
 Gene expression profiling
 Toxicological research (Toxicogenomics)
Advantages of DNA Microarray
 Provides data for thousands of genes in real time.
 Single experiment generates many results easily.
 Fast and easy to obtain results.
 Promising for discovering cures to diseases and cancer.
 Different parts of DNA can be used to study gene expression.
Disadvantages of DNA Microarray
 Expensive to create.
 The production of too many results at a time requires long time for analysis, which is quite
complex in nature.
 The DNA chips do not have very long shelf life.
DNA Array Technology in Nutrigenomics and Industry Applications

** Introduction to Nutrigenomics
Nutrigenomics is the study of how food and its components interact with our genes to
affect health.

It’s part of a broader field of nutrigenetics, which aims to understand the relationships
between genetics, diet, and health outcomes.

Nutrigenomics focuses on understanding how nutrients affect gene expression and

how individual genetic differences can influence the body's response to diet.
Key Concepts:
Nutrients and gene interaction: How specific nutrients can turn certain genes on or off,
influencing metabolic pathways, growth, immune function, and other processes.
Personalized nutrition: An emerging trend where individuals can receive tailored dietary
recommendations based on their unique genetic makeup, aiming to optimize health or manage
diseases.
Potential benefits: Addressing obesity, diabetes, cardiovascular diseases, and other chronic
conditions through customized diets.
** What is DNA Array Technology?
DNA array technology (or DNA microarray) is a powerful tool that allows researchers
to study the expression of thousands of genes simultaneously.

It’s widely used in genomics, including nutrigenomics, to analyze gene expression

patterns in response to different nutrients or dietary patterns.

Key Components of DNA Array Technology:

1. Probe (DNA fragments):
Thousands of specific DNA sequences are placed on a solid surface (often a glass
slide or silicon chip).
Each probe corresponds to a specific gene.
2. Target (Sample):
A sample of DNA or RNA from the subject is labeled with a fluorescent tag and applied
to the array.
This sample could be from a person’s blood or tissue, showing gene expression at that
moment.
 2. Hybridization:
The target DNA/RNA binds to the complementary probes on the array.
The degree of binding (hybridization) can indicate the level of gene expression.

3. Detection:
The intensity of the fluorescent signal is measured to determine which genes are active
and at what levels.
**Advantages of DNA Array Technology:**
High-throughput analysis:
Allows simultaneous examination of thousands of genes.
Insight into gene-diet interactions:
Provides a comprehensive view of how dietary components influence gene expression.
Disease association:
Helps in understanding the genetic predisposition to diseases linked to diet and how these
genes respond to different nutrients.
** DNA Array Technology in Nutrigenomics
In nutrigenomics, DNA arrays are used to:
1. **Gene Expression Profiling:**
- By using DNA arrays, researchers can measure how different foods, nutrients, or diets
influence the expression of thousands of genes in various tissues (such as the liver, adipose
tissue, or muscle).
- For example, a high-fat diet can trigger the expression of genes involved in lipid
metabolism, while certain antioxidants may downregulate genes related to inflammation.
2. **Identifying Biomarkers for Disease Risk:**
- DNA arrays help identify gene expression patterns that correlate with the risk of diseases
like obesity, diabetes, cardiovascular disease, and cancer.
- These genetic biomarkers can guide personalized dietary interventions to reduce disease
risk.
3. **Studying the Effects of Phytochemicals:**
- Nutrigenomics research often focuses on how natural compounds found in foods, like
polyphenols (from fruits and vegetables), affect gene expression.
- For instance, DNA arrays can reveal that polyphenols activate genes responsible for
antioxidant defense mechanisms.
4. **Elucidating Molecular Mechanisms:**
- DNA arrays can help to unravel the molecular mechanisms behind nutrient-gene
interactions, such as how omega-3 fatty acids suppress the expression of inflammatory genes.
5. **Understanding Metabolic Disorders:**
- In individuals with metabolic syndromes, DNA arrays can detect changes in gene expression
before symptoms arise, allowing early dietary interventions.
** Industry Applications of DNA Array Technology in Nutrigenomics
**1. Personalized Nutrition:**
- **Personalized diet plans**:
Companies are using DNA array technology to offer personalized dietary plans based on an
individual’s genetic profile.
Nutrigenomics tests provided by companies like **23andMe** or **Nutrigenomix** analyze
gene variants associated with metabolism, nutrient absorption, and disease risk.
This information is used to create dietary recommendations tailored to the individual’s genetics.
- **Custom supplements**: Some companies also use nutrigenomic data to develop
personalized supplements.
For instance, a person’s genetic makeup might suggest they are predisposed to vitamin D
deficiency, and they can be recommended a supplement accordingly.
**2. Functional Foods and Nutraceutical Development:**
- **Designing foods for gene health**:
DNA array technology allows food companies to identify nutrients that can
beneficially modify gene expression.
This insight helps in the development of **functional foods**—foods that provide
health benefits beyond basic nutrition.
Examples include foods fortified with omega-3s or specific antioxidants aimed at gene
modulation.
- **Nutraceutical industry**:
Nutraceutical companies are interested in developing products that can impact gene
expression.
For example, a product that activates longevity genes (such as **resveratrol** from
red wine, known for its effect on sirtuins) can be marketed as an anti-aging supplement.

**3. Disease Prevention and Management:**

- Nutrigenomics plays a significant role in managing chronic diseases through diet. DNA
array technology helps companies create dietary programs for conditions like diabetes or
cardiovascular disease based on an individual’s genetic predispositions and current gene
expression profiles.
**4. Weight Management Programs:**
Many companies are incorporating nutrigenomics into weight management.

For instance, **DNA fit** and other companies analyze genetic variants related to
metabolism, appetite regulation, and fat storage.

This data is used to suggest diets that may be more effective for weight loss or weight
maintenance in individuals based on their unique genetic profile.
**5. Consumer Genetic Testing Kits:**
DNA arrays are the foundation for many consumer-focused genetic testing kits in the
market, such as **AncestryDNA** and **23andMe**.
These tests often provide insights into how certain foods affect weight, cholesterol
levels, and even mental health, promoting personalized wellness strategies.
** Challenges and Ethical Considerations
**1. Ethical Concerns:**
- **Privacy:** The collection of genetic data raises concerns about privacy and data security.
There is a risk that genetic information could be misused by insurance companies or employers.
- **Equity in Access:** DNA array-based nutrigenomics services are often expensive,
which raises concerns about equitable access to personalized nutrition.
- **Genetic Determinism:** There is a risk that people may think they are “genetically
doomed” to certain conditions, which can lead to psychological stress or poor lifestyle choices
if not properly guided.
**2. Scientific Challenges:**
- **Complex Interactions:** The interaction between diet and genes is highly complex,
involving numerous genes and pathways. DNA array technology provides valuable
information, but understanding the full picture requires further research.
- **Environmental Influences:** Diet is not the only factor influencing gene expression.
Lifestyle factors such as physical activity, sleep, and stress also play significant roles.
** Future Trends
1. **Integration with Other Omics:**
- Nutrigenomics is likely to integrate with other “omics” fields like proteomics (study of
proteins) and metabolomics (study of metabolites) to provide a more comprehensive
understanding of gene-diet interactions.

2. **AI and Machine Learning:**

- The vast amount of data generated by DNA arrays can be analyzed more efficiently using
artificial intelligence (AI) and machine learning. These technologies will help identify complex
patterns in how diet affects gene expression, leading to even more personalized dietary
recommendations.

3. **Precision Agriculture and Food Supply:**

- DNA array technology can be used not only for human health but also to optimize the
nutritional content of crops and livestock, improving the quality of the food supply in line with
nutrigenomic principles.
** Conclusion
DNA array technology has revolutionized nutrigenomics by allowing researchers to
analyze the complex interactions between diet and genes.

In the industry, this technology is shaping personalized nutrition, functional foods, and
nutraceutical development.

While there are challenges and ethical considerations, the future holds great promise
for further integration of nutrigenomics into everyday life, potentially transforming
how we approach diet, health, and disease prevention.