Date written: October 25, 2026
Field: biology, molecular genetics, cell biology, philosophy of scientific explanation
Subject: deoxyribonucleic acid (DNA), its physical structure, the processes of copying and reading it, and its relationship to genes and RNA.
1. What DNA Is
Deoxyribonucleic acid (DNA) is a chemical macromolecule belonging to the class of nucleic acids. In cellular organisms, DNA is the principal material carrier of the inherited nucleotide sequence.
DNA is not an abstract code or an instruction existing separately from matter. It is a physical molecule formed from chemically bonded parts. Changing the sequence of its elements can influence which molecules are synthesized in a cell and which processes take place.
When biologists say that DNA “stores information,” they refer to a reproducible relationship between the order of nucleotides and the operation of molecular systems that use this order. The sequence itself does not perform transcription, create proteins, or independently determine the entire fate of an organism.
A clarification: the genetic material of some viruses is RNA, not DNA. Therefore, the assertion that “the hereditary material of every biological system must be DNA” is false.
2. What a DNA Molecule Consists Of
DNA belongs to the class of polymers: its long chains consist of repeatedly occurring structural units called nucleotides.
Each DNA nucleotide contains three chemical components:
- Deoxyribose, a five-carbon sugar.
- A phosphate group.
- A nitrogenous base, one of four principal variants.
| Symbol | Base | English name |
|---|---|---|
| A | Adenine | Adenine |
| T | Thymine | Thymine |
| G | Guanine | Guanine |
| C | Cytosine | Cytosine |
Nucleotides within one strand are joined by covalent phosphodiester bonds. Sugar and phosphate form a repeating backbone, while nitrogenous bases extend as its side components.
Consequently, the notation
5'-A T G C C A T G-3'
does not depict DNA in its entirety. It is a symbolic representation of the order of bases along one physical strand. The real molecule also contains sugars, phosphates, chemical bonds, spatial structure, and interactions with its environment.
Why DNA Is Called Deoxyribonucleic Acid
The name reflects its chemical organization: the sugar deoxyribose differs from RNA’s ribose by the absence of a hydroxyl group at the 2′ position; the polymer contains phosphate groups and belongs to the class of nucleic acids.
The word “acid” refers to the molecule’s chemical properties, not to its being necessarily corrosive or dangerous in its ordinary existence inside a cell.
3. Why DNA Is Usually Depicted as a Double Helix
Typical cellular DNA has a double-helix structure: two polynucleotide strands lie alongside one another and twist around each other.
Bases on opposing strands predominantly form complementary pairs:
- A with T, typically two hydrogen-bond contacts.
- G with C, typically three hydrogen-bond contacts.
A simplified diagram:
5'-A T G C C A T G-3'
| | | | | | | |
3'-T A C G G T A C-5'
The strands are oriented antiparallel: the 5′→3′ direction of one runs opposite to that of the other. These designations refer to carbon atom positions in the nucleotide’s sugar component.
Hydrogen bonds and interactions between adjacent bases contribute to the stability of the double helix. Under certain conditions, the strands can separate and then rejoin.
The double helix is a widespread, but not the only possible, organization of DNA: single-stranded DNA viruses, locally unwound DNA segments, and other spatial structures exist. A familiar illustration must not be turned into a universal form for all DNA under every condition.
4. Where DNA Is Located
In humans, most DNA is located in the cell nucleus, where it is organized into chromosomes. In addition to nuclear DNA, mitochondria possess a small amount of their own DNA.
An ordinary human somatic cell with a diploid nucleus contains 46 chromosomes, organized into 23 pairs. Germ cells contain a haploid set of 23 chromosomes.
A chromosome is not synonymous with a gene. It is an organized complex of a DNA molecule and associated proteins. In human cells, long DNA segments are wrapped around histone proteins to form nucleosomes, and subsequently larger structures of chromatin.
One chromosome contains numerous genes, intergenic regions, regulatory elements, and repetitive sequences.
A single haploid set of the human nuclear genome contains approximately 3.1–3.2 billion base pairs. An ordinary diploid cell contains two corresponding copies of most regions of the nuclear genome.
Not all cells of an adult human are organized alike: for example, mature human red blood cells lose their nuclei and mitochondria, and therefore contain no genome of their own.
5. What a Gene Is and How It Relates to DNA
A gene is a region of hereditary material identified by biological criteria and associated with the synthesis of functional RNA or a protein product (via RNA).
In the human body, most genes are regions of DNA.
The crucial distinction is:
- DNA is a physical molecule containing many sequences.
- A gene is an identified region of it corresponding to particular processes of expression and inheritance.
- An RNA transcript is a molecule produced when the relevant cellular systems read DNA.
- A protein is a possible result of subsequent reading of messenger RNA by a ribosome.
Genes do not lie inside DNA like separate objects in a container. They are regions of the DNA molecule itself; the boundaries and composition of a gene are determined from its sequence and experimental data on transcripts, splicing, and function.
Those boundaries are not always unambiguous. There are overlapping genes, alternative transcripts, different transcription start sites, and regulatory elements that act over long distances.
A Gene Does Not Have to Encode a Protein
Some genes are transcribed into messenger RNA (mRNA), which ribosomes use to synthesize proteins. Other genes produce noncoding RNAs, which participate in cellular processes themselves without being translated into proteins.
Examples of noncoding RNAs:
- ribosomal RNA (rRNA), a structural and functional component of the ribosome;
- transfer RNA (tRNA), which participates in protein synthesis;
- microRNAs (miRNAs), which regulate the availability and utilization of other RNAs;
- long noncoding RNAs (lncRNAs), a diverse group of transcripts with various interactions under investigation.
This is where LINC00662 belongs: it is a gene on human chromosome 19 whose transcription produces a long noncoding RNA. Its interactions are studied, for example, in neuronal and tumor cells.
6. How a Cell Uses a DNA Sequence
Three distinct processes must be distinguished: replication, transcription, and translation.
6.1. Replication: DNA → DNA
Replication is the process of synthesizing new DNA using existing DNA as a template.
Before cell division, the replication machinery separates regions of the two strands of the double helix. DNA polymerase enzymes attach new nucleotides to growing strands according to base complementarity.
Schematically:
Original double-stranded DNA
|
Strand separation
|
Synthesis of
new DNA strands
|
Two double-stranded DNA molecules
Each new double-stranded molecule contains one previously existing strand and one newly synthesized strand. This mechanism is called semiconservative replication.
DNA does not autonomously copy itself: the process requires enzymes, nucleotides, energy, and an organized cellular environment.
6.2. Transcription: DNA → RNA
Transcription is the synthesis of RNA using one of the DNA strands as a template.
Principal stages:
- Regulatory proteins and the transcription apparatus interact with a particular DNA region.
- RNA polymerase initiates RNA synthesis.
- It moves along the template DNA strand, adding ribonucleotides according to complementarity.
- An RNA transcript is produced.
- In eukaryotes, many transcripts undergo additional processing, such as splicing.
In RNA, the base uracil (U) is generally used instead of thymine.
Importantly, transcription does not mean that the entire DNA molecule is simultaneously “read.” It occurs in specific regions, cells, and conditions. Gene expression is regulated by numerous interacting factors.
6.3. Translation: mRNA → Protein
Translation is the process of synthesizing a polypeptide chain on a ribosome using the sequence of messenger RNA.
The ribosome reads the mRNA sequence in groups of three nucleotides called codons. Within the genetic code, these codons correspond to amino acids or signals terminating synthesis. Transfer RNAs help incorporate the corresponding amino acids into the growing chain.
The polypeptide may then fold, be modified, combine with other molecules, and participate in cellular processes.
Not every RNA is translated. For LINC00662, the relevant product is the noncoding RNA itself.
6.4. Diagram of Relationships
DNA
|
+-----------+-----------+
| |
Replication Transcription
| |
New DNA RNA
|
+-----------+-----------+
| |
Coding Noncoding
mRNA RNA
| |
Translation Interactions
| within the cell
Protein
This diagram represents the principal cellular processes, not a closed picture of every possible transfer of sequences. For example, reverse transcription enables DNA to be synthesized from an RNA template; retroviruses and certain cellular mechanisms use it.
7. Why DNA Sequence Influences Cellular Function
The chemical order of nucleotides matters because cellular molecules interact with particular sequences and structures.
Depending on context, a sequence can:
- determine the composition of synthesized RNA;
- influence a protein’s amino acid sequence through mRNA codons;
- participate in the binding of proteins that regulate transcription;
- influence splicing and subsequent RNA processing;
- serve as a recognition site for enzymes and other molecules.
However, the same DNA sequence does not imply the same expression of all genes in all cells. A neuron, muscle cell, and liver cell can contain almost identical nuclear genomes but have different expression profiles, proteins, chromatin states, and functions.
This is possible because the actual state of a cell depends not only on DNA sequence but also on numerous regulatory and metabolic processes.
“Genetic Information” and Its Material Realization
In scientific language, the word “information” is used to describe correspondences and dependencies established on the basis of molecular processes.
At least five things can be distinguished:
- Physical sequence: the real order of molecular components in DNA.
- Symbolic notation: representation of the sequence by A, T, G, and C.
- Rules of biological correspondence: for example, the relationship between mRNA codons and amino acids in the translation system.
- Functional outcome: a measured change in expression, protein composition, or cellular behavior.
- Interpretation: a researcher’s explanation of the observed change’s role in organismal development.
Calling an observed sequence an “instruction” can be a convenient way of designating certain relations. But an instruction does not exist as an independently acting entity that commands the cell to do anything.
8. What a Mutation Is
A mutation is a change in the sequence of genetic material. In DNA, this may be a substitution of one nucleotide, insertion, deletion, duplication, rearrangement of a larger region, or another alteration.
Causes include:
- errors in DNA copying;
- molecular damage and errors in repair;
- exposure to certain chemicals or radiation;
- movement of particular genetic elements;
- other cellular and external processes.
A mutation does not automatically mean disease or beneficial adaptation. Its consequences may be absent, apparent only in a particular environment, or dependent on the combination of numerous factors.
One sequence variant may affect the production of a particular RNA, another the properties of a protein, and a third the binding of regulatory molecules. The existence of a change does not yet establish its function or clinical significance.
Nor should every mutation be equated with transmission to descendants: a change in a somatic cell can remain within its cell lineage, whereas transmission to the next generation ordinarily requires the involvement of the relevant genetic material of germ cells.
9. What Epigenetic Regulation Is
Nucleotide sequence is not the only property of DNA that can matter for expression.
Cells can change the chemical state of DNA and of proteins interacting with it. Mechanisms under investigation include:
- DNA methylation;
- histone modifications;
- nucleosome movement and remodeling;
- interactions of regulatory RNAs and proteins with chromatin.
Such changes can alter the accessibility of DNA regions and their transcription levels without changing the A, T, G, and C sequence itself.
This does not mean that methylation always “switches off a gene”: the effect depends on where the change occurs and in what cellular context it is observed.
Some epigenetic states persist through cell divisions, but this is not equivalent to universal inheritance of all acquired changes across generations of organisms.
Example: LINC00662 and PTERV1
A study of comparative LINC00662 expression discusses a retroviral insertion, PTERV1, located near this gene in the chimpanzee genome.
In the cell models studied, the insertion is associated with epigenetic suppression of LINC00662 expression. After experimental deletion of the insertion using CRISPR-Cas9, gene expression was restored.
This reveals distinctions between several levels at once:
- DNA sequence: the presence or absence of the PTERV1 insertion.
- Chemical state of DNA: methylation of particular regions.
- Gene expression: detection or suppression of LINC00662 RNA.
- Cellular effects: changes associated with the development of neuronal models.
- Evolutionary interpretation: the mechanism’s possible contribution to differences between human and chimpanzee lineages.
Evidence for a dependence between the first and third levels is not automatically evidence for the origin of human thinking.
See the separate article on LINC00662.
10. Differences Between DNA and RNA
| Feature | DNA | RNA |
|---|---|---|
| Full name | Deoxyribonucleic acid | Ribonucleic acid |
| Sugar | Deoxyribose | Ribose |
| Principal bases | A, T, G, C | A, U, G, C |
| Typical organization | Two complementary strands | One strand, capable of forming complex secondary structures |
| Common cellular role | Storage and transmission of inherited sequence | Gene expression, regulation, and numerous structural and catalytic functions |
| Synthesis | DNA polymerases and other systems | RNA polymerases and other systems |
| Exceptions | Single-stranded DNA exists; some viruses use DNA | Double-stranded RNAs exist, including in viruses |
One cannot conclude that “DNA is always storage, while RNA is always an intermediary.” This describes characteristic roles, not the exhaustive essence of the two classes of molecules.
11. What DNA Does Not Explain by Itself
The popular description of DNA as the “blueprint of an organism” creates the impression that merely discovering the nucleotide sequence is sufficient to unambiguously derive a person’s structure, behavior, and inner life.
That transition requires additional grounds.
11.1. Sequence and Organismal Development
DNA participates in organismal development through real cellular processes. Development, however, takes place under specific spatial, temporal, chemical, and physiological conditions.
The sequence is not identical to the process of development. An observed dependence on a particular genomic region does not make that region the sole cause of a complex trait.
11.2. Gene and Function
When someone says “gene X is responsible for Y,” it is necessary to establish:
- which specific gene or sequence variant was studied;
- in which cells and conditions;
- what exactly the researchers changed;
- which indicator was measured;
- how reproducible the result is;
- on what grounds the observed cellular effect is connected to a more complex phenomenon.
A statistical association with a trait is not equivalent to establishing the complete mechanism of its emergence.
11.3. DNA and Human Thinking
Discovering a molecular mechanism of neuronal development is not the same as explaining thinking, consciousness, speech, or subjectivity.
A study may establish that intervening in a particular DNA region changes RNA levels, neurite growth, or neural-network activity. The next thesis, “this region explains human thinking,” is already a separate assertion, requiring investigation of the transition between these phenomena.
Expressions such as “intelligence gene,” “aggression gene,” and “behavior gene” can replace the relations under investigation with ready-made categories if the relevant trait is not concretely defined and the actual results are not specified.
12. Fundamental Distinctions
| What is distinguished | First | Second |
|---|---|---|
| Molecule and representation | DNA as a chemical structure | A string of A, T, G, C written by a researcher |
| Whole and region | DNA as a polymer and part of the genome | A gene as a designated region of genetic material |
| Gene and product | A sequence used during expression | Synthesized RNA and, sometimes subsequently, a protein |
| Sequence and state | Order of bases | Methylation, chromatin packaging, and other changes |
| Process and designation | Particular transcription or translation | The figurative expression “DNA gave a command” |
| Observation and interpretation | Measured expression or cellular effect | Explanation of the role in an organism, behavior, or evolution |
| Biological causality and teleology | Measured dependencies | The claim that a gene “exists for” a predetermined purpose |
These distinctions enable investigation of real mechanisms without transforming explanatory labels into independently acting entities.
13. Brief Definitions
Nucleotide: a chemical structural unit of a nucleic acid containing a sugar, base, and phosphate.
DNA: a nucleotide polymer, usually organized in cells as a double helix and used as the principal hereditary material.
Gene: a region of hereditary material associated with the production of functional RNA or, through RNA, a protein.
Genome: the totality of genetic material of an organism or another biological system under consideration.
Chromosome: an organized structure containing a DNA molecule and, in cells, proteins associated with it.
Replication: copying DNA by synthesizing new complementary strands.
Transcription: synthesis of RNA from a DNA template.
Translation: synthesis of a protein according to a messenger RNA sequence.
Gene expression: the processes producing gene products and regulating their quantities.
Mutation: a change in the sequence of hereditary material.
Epigenetic regulation: changes in regulation and stable cellular states that do not require replacing the DNA sequence itself.
14. Sources
- National Human Genome Research Institute (NHGRI). Deoxyribonucleic Acid (DNA). Genetics glossary. https://www.genome.gov/genetics-glossary/Deoxyribonucleic-Acid-DNA
- NHGRI. Nucleotide. https://www.genome.gov/genetics-glossary/Nucleotide
- NHGRI. Base Pair. https://www.genome.gov/genetics-glossary/Base-Pair
- NHGRI. A Brief Guide to Genomics. https://www.genome.gov/about-genomics/fact-sheets/A-Brief-Guide-to-Genomics
- MedlinePlus Genetics, U.S. National Library of Medicine. What is DNA? https://medlineplus.gov/genetics/understanding/basics/dna/
- MedlinePlus Genetics. What is a gene? https://medlineplus.gov/genetics/understanding/basics/gene/
- Alberts B. et al. Molecular Biology of the Cell. Section The Structure and Function of DNA. NCBI Bookshelf. https://www.ncbi.nlm.nih.gov/books/NBK26821/
- NHGRI. Nucleic Acids. https://www.genome.gov/genetics-glossary/Nucleic-Acids
- See also: LINC00662: noncoding RNA, brain development, the PTERV1 retrovirus, and oncology.
Conclusion
DNA is a physical molecule, not a ready-made explanation of an organism. Its sequence participates in inheritance and cellular function through copying, transcription, regulation of expression, and the interactions of numerous molecular systems.
A gene is not a separate object inside DNA but a particular region of hereditary material. A gene product arises in a process carried out by the cell. In some cases, it is RNA used for protein synthesis; in others, it is the functional noncoding RNA itself.
Between establishing a molecular dependence and explaining a complex biological or cognitive phenomenon lies an independent research transition. That transition must not be replaced by phrases such as “DNA programmed it,” “the gene is responsible,” or “evolution created it” if the relevant causal relations have not yet been revealed.
