In this blog post, I’ll explain the principles behind DNA chips, the manufacturing process, and their real-world applications in an easy-to-understand way.

Background and Basic Concepts of DNA Chips

The Human Genome Project, launched in 1990, attracted widespread attention. When the project announced on April 14, 2003—ahead of schedule—that it had sequenced approximately 99% of the entire genome with 99.99% accuracy, expectations soared that various intractable diseases, such as Alzheimer’s and diabetes, would be cured in a short time. However, even though the genome sequence had been completed, much remained unknown about how each gene is expressed and what functions it performs; consequently, the importance of technologies for measuring and interpreting gene expression grew significantly. Amid this, DNA chips gained attention as tools capable of observing gene expression on a large scale simultaneously.
A DNA chip is a device in which hundreds to hundreds of thousands of short DNA fragments (or cDNA) are immobilized in a small grid pattern on a solid surface, such as glass or a semiconductor. At each location, a probe with a sequence complementary to a specific gene is immobilized; when target nucleic acids from a sample bind to it, a signal is generated at that location, indicating which genes are expressed and to what extent. In other words, it can be described as a kind of “gene panel” that reads the expression patterns of many genes at once.

The Process of Gene Expression and the Principles Behind DNA Chip Production

A gene refers to a specific section of DNA that encodes the amino acid sequence that makes up a protein. For a gene to actually function and produce a protein, it must undergo two main stages: transcription—the process of transferring information from DNA to mRNA—and translation—the process of synthesizing a protein based on that mRNA information. DNA chips focus on the transcription process, which reveals the amount of active genes in a cell, specifically by observing changes at the mRNA level.
The transcription process generally proceeds through the following stages. First, during the initiation stage, RNA polymerase binds to specific sites on the DNA—such as the promoter—and prepares to begin RNA synthesis. Next, during the elongation stage, RNA polymerase unwinds the double-stranded DNA and synthesizes a complementary RNA strand using one strand as a template. Finally, in the termination phase, once synthesis is complete, the resulting precursor mRNA (pre-mRNA) undergoes processing within the cell. During this process, regions called introns—which are not part of the actual protein code—are removed, and only the exons are spliced together to form mature mRNA.
It is important to note that the presence of mature mRNA in a cell serves as direct evidence that the corresponding gene is being expressed. Therefore, by measuring mRNA levels, we can determine which genes are active and to what extent. However, since mRNA is difficult to directly immobilize on a chip, it is generally synthesized into complementary DNA (cDNA) via reverse transcription.
Reverse transcription was inspired by the process involving reverse transcriptase found in retroviruses (e.g., certain tumor viruses or HIV). Retroviruses use their own reverse transcriptase enzyme to transcribe their RNA genetic material into DNA, which they then insert into the host genome to replicate. Researchers use this reverse transcriptase to create cDNA complementary to mature mRNA within cells, and then immobilize (or synthesize) that cDNA on the surface of a solid-phase chip to use it as a probe.
In summary, DNA chips work by converting mRNA obtained from cells into cDNA through reverse transcription, then arranging this cDNA or synthesized oligonucleotides on the chip to bind with the nucleic acids in the target sample. The degree of binding is detected using methods such as fluorescent labeling, allowing for quantitative comparison of gene expression levels.

Major Applications and Expected Benefits of DNA Chips

1) Gene discovery: DNA chips are widely used to rapidly identify genes that exhibit expression differences across different tissues or under different conditions. They are highly effective in discovering genes with unknown functions by comparing them to previously known expression patterns or by identifying genes newly activated under specific conditions. Additionally, they allow for the simultaneous observation of changes in expression over time or responses to drug treatment, enabling the inference of interactions between genes.
2) Clustering Analysis: Clustering analysis, which groups large-scale gene expression data based on similarity, is useful for identifying genes with similar expression patterns and inferring their functions. Since groups of genes that are co-expressed under similar conditions often play similar biological roles or are involved in the same pathways, the functions of unknown genes can be predicted based on these clusters. This approach provides important clues for understanding complex biological networks.
3) Disease Diagnosis and Identification of Causes: Most diseases arise from the interaction of multiple genes. Since DNA chips allow for the simultaneous observation of gene expression patterns across thousands to tens of thousands of genes, they help identify disease-specific expression patterns for diagnostic purposes or determine the underlying causes of diseases. They can also be used to monitor treatment responses or develop personalized therapies for patients.
So far, we have examined the basic principles, manufacturing process, and representative applications of DNA chips. As DNA chips enable the large-scale observation of gene functions and expression patterns—which are difficult to discern from genomic sequence data alone—significant progress is being made in both life science research and medical diagnostics.
DNA chip technology enables us to understand biological information more systematically and holds great potential to ultimately contribute to the improvement of human health. We look forward to further advancements in research and applications based on this technology, which will provide tangible benefits in clinical and public health settings.