The Story of Paternity Testing ① The Story of DNA

Rewritten on: June 16, 2025

A clear explanation of DNA's double-helix structure and base sequences (A, T, G, C). From the basics of polymers, nucleotides, and base pairs to why base sequences are used in DNA testing (paternity testing), seeDNA's specialist staff explain it carefully.

Introduction

I'd like to explain, over several installments, the concepts behind the DNA testing used in our high-accuracy paternity testing, using as plain language as possible. It's greatly simplified, so any experts reading this might get a bit annoyed.

First, I'll explain the shape and characteristics of DNA. After that, I'd like to talk about the actual thinking behind DNA testing. Some difficult terms will come up, but I'll try to explain them as clearly as possible. If you don't understand, that's on me as the writer.

The word "DNA" comes up often in the news and dramas, but surprisingly few people actually understand precisely what shape it takes and how it works. For anyone considering DNA testing, having a basic understanding of DNA is an important first step toward correctly interpreting the results. In this article, I'll break down everything from the physical structure of DNA to how base sequences are read, as simply as possible, so please read to the end.

Today, DNA testing is used not only to confirm parent-child relationships but also across an extremely wide range of fields, including criminal investigations in forensic medicine, personal identification, and screening for hereditary diseases. Underlying all of these applications is the "individually unique base sequence pattern" that the DNA molecule carries, and understanding this mechanism helps in correctly interpreting accurate test results. I hope that through this article, your vague impression of DNA can be updated into a scientific understanding.

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The Shape and Characteristics of DNA

The following is a quote from Wikipedia.

Deoxyribonucleic acid (DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. This polymer carries the genetic instructions for the development, functioning, growth, and reproduction of all known organisms and many viruses. [ref:1]

Source: "Wikipedia, the Free Encyclopedia," Japanese edition

Let's try working through this starting with "polymer." Roughly speaking, a polymer is a large substance made up of many monomers. A monomer is a small substance with similar properties. The "mono" in monomer comes from the English "mono-," meaning "one." It's the same "mono" as in monorail or monotone.

Polymers are named by adding "poly" before the monomer's name. So a polynucleotide chain is a straight, chain-like substance whose monomer is the nucleotide. Incidentally, it also has directionality (often written as 5'→3'). When it exists as DNA, the two polynucleotide chains line up in opposite directions and wind around each other, forming a shape like a spiral staircase (the lower half of the figure).

To be a bit more specific, a nucleotide is made up of three parts: a "sugar (deoxyribose)," a "phosphate," and a "base." The sugars and phosphates alternate to form the "backbone" of the DNA, with bases sticking out sideways from it. Because this backbone is joined by strong covalent bonds called phosphodiester bonds, DNA is a chemically very stable molecule capable of holding genetic information over a long period. [ref:5]

This helical structure is called a "double helix", and the model published in 1953 by James Watson and Francis Crick is the most famous. This achievement of discovering the double helix is considered the starting point of molecular biology, and it was groundbreaking for understanding how genetic information is stored and transmitted. [ref:2] Their research relied heavily on X-ray diffraction data obtained by Rosalind Franklin, and it's said that without the image known as "Photo 51," building the double helix model would not have been possible. [ref:6]

In everyday life, "DNA" is sometimes used to mean almost the same thing as "gene," but strictly speaking, DNA refers to the substance itself, while a gene refers to a specific region on the DNA where the blueprint information for a protein is recorded. Human DNA contains about 3 billion base pairs, but the gene regions that code for proteins make up only about 1.5% of the total. The rest was once called "junk DNA," but recent research has increasingly revealed that it plays important roles, such as regulating gene expression. [ref:3] In particular, the results of the ENCODE (Encyclopedia of DNA Elements) project, published in 2012, suggested that about 80% of the human genome may have some kind of biochemical function, forcing a major revision of the conventional "junk DNA" concept. [ref:7]

What Is a DNA Base Sequence?

Let's take a closer look at DNA using the diagram quoted from Wikipedia [ref:1].

In the diagram, the chain of the polynucleotide chain (called the main chain) is drawn as a light blue ribbon. Inside the ribbon, the pentagon labeled S for the sugar and the circle labeled P for the phosphate alternate. From each sugar in the chain, one of the four nitrogen-containing bases (cytosine: C, guanine: G, adenine: A, thymine: T) sticks out sideways, as if in an image. The bases A and T, or C and G, are chemically compatible and form a pair called a base pair (shown in the smaller box in the center of the diagram). Centered on these base pairs, the two polynucleotide chains line up in opposite directions to form double-stranded DNA.

This base-pairing rule (A with T, G with C) is also known as "Chargaff's rule," and it is the fundamental mechanism that enables DNA to be replicated accurately. In 1950, Erwin Chargaff discovered that, across virtually all species, the amount of adenine in DNA is nearly equal to the amount of thymine, and the amount of guanine is nearly equal to the amount of cytosine. [ref:5] This discovery became an important clue for Watson and Crick in building their double-helix model.

When a cell divides, the double strand temporarily unwinds into single strands, and each strand serves as a template for synthesizing a new complementary strand. Because T is always placed opposite A, and C is always placed opposite G, two complete sets of double-stranded DNA, identical to the original, are produced.

Additionally, two hydrogen bonds form between A and T, while three hydrogen bonds form between G and C. Because of this difference, the G-C bond is somewhat stronger than the A-T bond. The higher the proportion of G-C in a given stretch of DNA, the higher the temperature (melting temperature, or Tm value) required to separate the double strand. This property is important in setting conditions for laboratory DNA analysis and PCR (polymerase chain reaction). [ref:5]

What's commonly called base sequence analysis in DNA testing is the process of reading the order of the bases, that is, the sequence of G, A, T, and C. The base sequence is read in the 5'→3' direction. Using the diagram as an example, on the left polynucleotide chain, the 5'→3' direction runs from top to bottom, so it reads AGTACG. As for the right-hand polynucleotide chain... in fact, except in special cases, it's often not even read. That's because A always pairs with T, and G always pairs with C, so both polynucleotide chains carry the same information.

To simplify the last line of the Wikipedia quote, I think it's enough to understand it this way: "DNA is a blueprint for living organisms, a book written in just four letters: G, A, T, and C."

In other words, human^※ DNA holds all the information needed to create a human being.

※ Writing "human" (ヒト) in katakana refers to the organism without personhood, as a way to distinguish it from "person" (人), which carries personhood.

As a side note, a DNA base sequence doesn't directly function as a "blueprint for proteins" on its own. Genetic information in DNA is first "transcribed" into mRNA (messenger RNA), and then the information in the mRNA is "translated" at the ribosome to synthesize a protein. This one-directional flow of information was called the "central dogma" by Francis Crick, and it is a foundational principle of molecular biology. [ref:6] DNA testing does not analyze these protein-coding regions; instead, it primarily analyzes repeat sequences (STRs) located in non-coding regions, which allows for accurate identification while protecting individual privacy.

Why Base Sequences Are Used in DNA Testing

So far, we've covered the basics of DNA's structure and base sequences, but why can this base sequence be used for DNA testing (paternity testing)? There are two main reasons.

• Sequence patterns that differ from person to person exist ― Most of human DNA is nearly identical across all of humanity, but certain regions contain repeat sequences (STR: Short Tandem Repeat) that differ between individuals. By comparing the differences in the number of these repeats, individuals can be identified with high precision. [ref:4] An STR is a short sequence unit of 2 to 6 bases repeated anywhere from a few times to several dozen times; for example, a 4-base sequence like "AGAT" might repeat 8 times in one person and 12 times in another. In DNA testing, typically 15 to 20 or more STR regions are analyzed simultaneously, making it possible to effectively distinguish every individual except identical twins. [ref:5]
• The rules of inheritance from parent to child are clear ― A child inherits half of their DNA from their father and half from their mother. This is the basic principle of inheritance based on Mendel's laws, and for each STR region, a child receives one allele from the father and one from the mother. Therefore, by comparing a specific STR region between parent and child, it's possible to clearly determine "whether this repeat pattern comes from the father or the mother," providing scientific proof of a parent-child relationship.
• Testing technology is highly established ― PCR (polymerase chain reaction) technology can amplify STR regions by millions of times even from a tiny DNA sample, allowing for analysis. Furthermore, using capillary electrophoresis makes it possible to accurately measure the length of the amplified DNA fragments (that is, the number of STR repeats) with base-pair-level precision. [ref:2]

In short, at the core of DNA testing is "the technology to accurately read individual differences in base sequences," and it's this technology that enables DNA analysis to be used across such a wide range of fields, from criminal investigations in forensic medicine to confirming family relationships and even assessing the risk of hereditary diseases. [ref:2]

An important indicator for understanding the accuracy of DNA testing is the "Probability of Paternity." This is a statistically calculated probability that the tested man is the child's biological father, and when the value obtained is typically 99.99% or higher, the conclusion is that "paternity is confirmed." Conversely, if mismatched patterns are found between parent and child across multiple STR regions, the conclusion reached is that "paternity is excluded." seeDNA uses internationally certified STR marker sets to ensure high accuracy and reliability.

Basic Terminology for DNA Testing

Here, let's organize the key terms that have come up in the explanation so far. This will be useful when researching DNA testing or reading a results report.

1. DNA (deoxyribonucleic acid) ― The double-stranded macromolecule that carries genetic information. It exists in the nucleus of every cell. In humans, a single cell nucleus contains about 6 billion base pairs of DNA (combined from the father and mother), which, if stretched out entirely, would be about 2 meters long.
2. Nucleotide ― The smallest building block (monomer) of DNA. It consists of three parts: a sugar (deoxyribose), a phosphate, and a base. Depending on the type of base, it may be distinguished as an adenine nucleotide, thymine nucleotide, and so on.
3. Base pair ― A pair formed by hydrogen bonds between A and T, or G and C. It is the structural foundation that stabilizes the double helix. The size of the human genome is expressed as about 3 billion base pairs (3×10⁹ bp).
4. Double helix ― The characteristic three-dimensional structure of DNA, in which two polynucleotide chains twist around each other in opposite directions. It completes one turn roughly every 10 base pairs, and the diameter of the helix is about 2 nanometers.
5. STR (Short Tandem Repeat) ― A region where a short sequence of about 2 to 6 bases repeats. The number of repeats differs from person to person, making it the primary target analyzed in paternity testing. The CODIS database maintained by the FBI (Federal Bureau of Investigation) uses 20 STR markers as its standard set. [ref:5]
6. Base sequence analysis (sequencing) ― The technology for reading the order of A, T, G, and C. With the advent of next-generation sequencers (NGS), it has become possible to decode large amounts of DNA information quickly and at low cost. [ref:3] Today, it's even technically possible to decode an individual's entire human genome within a few days.
7. PCR (polymerase chain reaction) ― A technology that amplifies a specific DNA region by millions of times. It was developed in 1983 by Kary Mullis and is widely used not only in DNA testing but also in medical diagnostics and infectious disease testing. [ref:6]

Just knowing these basic terms should make it much easier to understand a DNA test results report or an explanation of how the testing works.

The Mechanism of DNA Replication and Its Relation to Testing Accuracy

One of the most important biological implications of DNA's double-helix structure is that it enables "semiconservative replication." The experiment conducted by Meselson and Stahl in 1958 demonstrated the model of "semiconservative replication," in which, during DNA replication, the double strand completely unwinds and each strand serves as a template for synthesizing a new complementary strand. [ref:6] Thanks to this mechanism, the roughly 37 trillion cells that make up our bodies each retain nearly identical DNA information.

The reason this fact matters for DNA testing is that the same DNA information can be obtained from cells taken from any part of the body. Whether from cells in the oral mucosa, white blood cells, or hair root cells, the repeat pattern of STR regions is essentially the same. This is why reliable DNA testing can be performed using an easy-to-collect oral swab, or even from indirect samples such as hair, nails, or a toothbrush.

That said, DNA replication is not carried out with 100% perfection. Rarely, a "mutation" can occur during the replication process. In DNA testing as well, if a mismatch is observed in one or two STR regions between parent and child, it's necessary to carefully determine whether this is due to a mutation or genuinely indicates the absence of a parent-child relationship. seeDNA analyzes multiple STR regions simultaneously and performs a comprehensive assessment using statistical methods that also account for the possibility of mutation.

The History of DNA Testing and Technological Progress

The history of DNA testing began in 1984, when British geneticist Alec Jeffreys developed "DNA fingerprinting." [ref:5] Jeffreys discovered that a specific region of human DNA (minisatellites) varies greatly between individuals, and showed that this could be applied to personal identification. This technology was first applied to a murder investigation in the UK in 1986, contributing both to identifying the suspect and to preventing a wrongful conviction.

Later, in the 1990s, the spread of PCR technology made it possible to perform testing even from tiny DNA samples, and the establishment of STR analysis methods completed the highly accurate paternity testing and personal identification technology used today. In modern DNA testing, an accurate STR profile can be obtained even from the DNA contained in just a few cells, through the combination of PCR amplification and capillary electrophoresis.

In recent years, the cost of next-generation sequencing (NGS) technology has been rapidly declining, and in addition to conventional STR analysis, more advanced testing that combines SNP (single nucleotide polymorphism) analysis and whole-genome analysis is increasingly becoming practical. [ref:7] This is further improving testing accuracy for degraded or mixed samples, and DNA testing technology continues to evolve even now.

Frequently Asked Questions

Q1. What kind of structure is DNA's "double helix"?

A. A double helix is a three-dimensional structure in which two polynucleotide chains line up in opposite directions and twist around each other like a spiral staircase. The strands are joined on the inside by hydrogen bonds between base pairs (A with T, G with C), and this structure allows DNA to stably store genetic information. This model, proposed by Watson and Crick in 1953, forms the foundation of modern molecular biology and DNA testing technology. It completes one turn roughly every 10 base pairs, with a precise structure whose helix diameter is about 2 nanometers.

Q2. What roles do the four bases A, T, G, and C play?

A. The four bases—adenine (A), thymine (T), guanine (G), and cytosine (C)—are the "letters" that write out DNA, the "blueprint of life." The order in which these four letters appear (the base sequence) conveys the blueprint information for proteins and genetic instructions. Because A always pairs with T and G always pairs with C, following a complementarity rule (Chargaff's rule), a mechanism exists for DNA to be copied accurately during cell division. Note that A and T are joined by two hydrogen bonds, while G and C are joined by three, which is a key difference between them.

Q3. What part of DNA does DNA testing examine?

A. What's primarily examined in paternity testing are regions called STRs (Short Tandem Repeats), which are short repeating base sequences. The number of these repeats differs from person to person, and a child always inherits one set from the father and one from the mother. By comparing 15 to 20 or more STR regions simultaneously, it's possible to determine paternity with an accuracy of 99.99% or higher. Because STRs exist in non-coding regions, testing can be performed without revealing personal health information such as hereditary disease risk.

Q4. Are DNA and genes the same thing?

A. Strictly speaking, they are different. DNA refers to the substance itself that stores genetic information, while a gene refers to the specific region on DNA where the blueprint information for a protein is encoded. Human DNA contains about 3 billion base pairs, but the gene regions that code for proteins make up only about 1.5% of the total. It's known that the remaining regions also have important functions, such as regulating gene expression, and the reassessment of what was once called "junk DNA" continues to progress.

Q5. How is a sample collected for DNA testing?

A. The most common method is to lightly rub the inside of the mouth's mucous membrane with a dedicated cotton swab. It's nearly painless and finishes quickly. In addition to oral swabs, seeDNA also accommodates a variety of samples such as hair, nails, and toothbrushes, and proposes the optimal testing method based on each customer's situation. Collection kits can also be mailed to your home. Since the DNA information obtained is essentially the same regardless of which part of the body the cells are taken from, any sample type yields highly reliable results.

Q6. Are DNA test results legally valid?

A. To use DNA test results for legal purposes, the test must be conducted following a strict procedure called "legal testing." Legal testing requires that a third party be present during sample collection, that identity verification be performed, and that proper chain-of-custody records for the samples be maintained. seeDNA also offers legal testing and issues test reports that can be submitted to a court.

Q7. Is DNA testing possible for identical twins?

A. Because identical twins develop from the same fertilized egg, their STR region patterns are nearly identical. It has traditionally been difficult to distinguish identical twins using STR analysis alone, but in recent years, efforts have been made to detect the slight genetic differences between identical twins by also using SNP (single nucleotide polymorphism) analysis and somatic mutation detection technology.

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Author

Staff Member A, Parent-Child DNA Testing (STR)

Affiliation: seeDNA Co., Ltd., Testing Department

[References]

(1) Wikipedia, February 2003
(2) Nature, April 1953
(3) From parent-child relationships to criminal investigations, hereditary disease risk, and ancestry analysis, May 2025
(4) Ishosha JP, March 2018
(5) Nature, September 2012
(6) PR TIMES - No. 1 in press release distribution and sharing, September 2022