1959 Nobel Prize in Physiology or Medicine — Ochoa and Kornberg: Synthesizing DNA and RNA in a Test Tube

What You Will Learn in This Article

Six years after the publication of the DNA double helix, this article explains how Ochoa discovered an enzyme that synthesizes RNA in a test tube, and how Kornberg discovered an enzyme that synthesizes DNA. It also explains how these two discoveries became the experimental roots of today’s PCR, mRNA vaccines, and genetic engineering.

Beyond Common Sense: From Structure to Machine

The DNA double helix (published in 1953) was a pivotal event in 20th-century biology, but it did not, in itself, show "how this helix is actually replicated." Watson and Crick’s model presented the concept of complementary base pairing (A-T, G-C) and provided a conceptual basis for replication, but the identity of the molecular machine that actually performs this replication inside a cell remained an open question.

In 1958, Matthew Meselson and Franklin Stahl demonstrated, through a famous experiment (using heavy nitrogen labeling), that DNA replication is semiconservative – each daughter DNA strand consists of one strand from the parent and one newly synthesized strand. However, who actually does the synthesizing? remained unknown.

Kornberg’s 1956 experiment provided an answer to this question. He isolated an enzyme from E. coli that he named DNA polymerase, and demonstrated that this enzyme actually synthesizes DNA in a test tube. Although it was in a test tube and not inside a living cell, it established that DNA replication is a chemically reproducible reaction.

Ochoa’s discovery came from a different direction. The enzyme he discovered in 1955, called polynucleotide phosphorylase, could synthesize RNA in a test tube. Although this enzyme actually functions to break down RNA in nature, under experimental conditions, it reverses the reaction and synthesizes RNA. This discovery provided humanity with a tool to synthesize RNA in a test tube and arbitrarily control its composition, which later became the experimental basis for deciphering the genetic code.

Expressed in the language of CS, the two discoveries are as follows: if the double helix revealed the storage format of information, then Kornberg and Ochoa discovered the hardware that copies and prints the stored information. Printing is impossible without a storage format, and storage is meaningless without printing hardware. Both pieces must be present for the information system to function.

The Zeitgeist: A Year of Turmoil

1959 was a year of repeated political upheavals in various regions.

In January, the Cuban Revolution succeeded. Fidel Castro’s guerrilla forces entered Havana and the Batista regime collapsed. This event became a crucial factor in US-Latin American relations and the Cold War for decades. In March, the Tibetan uprising against China occurred, and after its suppression, the Dalai Lama fled to India. In September, Khrushchev made an official visit to the United States. This was the first official visit to the United States by a Soviet leader, and marked the beginning of détente.

During this period, molecular biology in American universities was experiencing explosive growth. Stanford, MIT, Columbia, and NYU were at the forefront of this trend, and Kornberg moved from the University of Washington to Stanford during this period, making his laboratory a central hub of molecular biology at Stanford.

When viewed in conjunction with Korean history, 1959 was the prelude to the April 19 Revolution of the following year. The Rhee Syngman regime was preparing for a rigged election, and social discontent was reaching a critical point.

Kornberg: Extracting DNA Synthesis Enzymes from E. coli

Arthur Kornberg was a Jewish man born in Brooklyn, New York. He trained at NYU and then established himself at the University of Washington (St. Louis). He later moved to Stanford University in 1959, the year he won the Nobel Prize, and spent the rest of his life there.

His experimental protocol was detailed, but conceptually, it followed this flow:

Step 1: E. coli cells were lysed to obtain a cell extract. This contains various enzymes from the cell.

Step 2: DNA fragments (template), four types of nucleotides, and an energy source (ATP) were added to this extract and reacted under specific conditions.

Step 3: After the reaction, it was confirmed whether new DNA had been synthesized. If radiolabeled nucleotides were used, radioactivity would be detected in the newly synthesized DNA.

The results were clear. The cell extract actually synthesized new DNA and accurately copied the sequence of the given template. Kornberg purified the enzyme responsible for this activity and named it DNA polymerase I (Pol I).

Although this discovery was crucial, it was not yet a complete picture. Kornberg’s Pol I turned out to be primarily responsible for DNA repair in cells, and the actual replicator, Pol III, was discovered a few years later. However, the fact that Kornberg established the experimental basis for creating DNA in a test tube was crucial.

Ochoa: A Serendipitous Discovery of RNA Synthesis

Severo Ochoa was born in Asturias, Spain. He trained in Madrid and built an international career, attending Heidelberg, Oxford, and NYU. He settled in the United States in 1929 to escape the Spanish Civil War and spent most of the rest of his life at NYU.

His 1955 discovery was almost accidental. He was studying the chemistry of phosphate bonds in cellular energy metabolism and observed that an enzyme obtained from spinach leaves degraded RNA. In order to accurately identify the properties of this enzyme, he tried various experimental conditions and discovered that, under specific conditions (high concentrations of nucleoside diphosphates), this enzyme reversed its reaction and synthesized RNA.

This enzyme is polynucleotide phosphorylase. As the name suggests, it is actually a phosphate-cleaving enzyme, but it can synthesize RNA by reversing the reaction under certain conditions.

The practical value of this discovery was immediately apparent. It became possible to synthesize the desired composition of RNA in a test tube. By controlling the ratio of specific nucleoside diphosphates, the experimenter could obtain RNA of a specific composition. For example, if only uracil diphosphate was added, poly-U (RNA consisting only of U) was obtained.

This tool became the first experimental key to decoding the genetic code. In 1961, Marshall Nirenberg and Heinrich Matthaei, using Ochoa’s method, observed that poly-U RNA created in a test tube produced poly-phenylalanine (a protein consisting only of phenylalanine) when added to a cell extract. This observation established the first genetic code correspondence: UUU = phenylalanine.

Ochoa’s team subsequently elucidated several other codon-amino acid correspondences using this method, and the genetic code was completely deciphered (1968 Nobel Prize, Nirenberg, Holley, and Khorana).

CS Framework of Copier and Printer

Now, let’s integrate the two discoveries using the language of CS.

DNA polymerase = copier. It accurately copies DNA from a template to create new DNA. This is essential for passing the entire genome to the next generation during cell division. It can be considered the permanent storage backup hardware of the system.

RNA polymerase = printer. After Ochoa’s discovery, the actual RNA polymerase in cells (the RNA polymerase of E. coli was established around 1960) was identified, completing the picture of how RNA is made. This enzyme uses DNA as a template to create RNA copies. It is a printer that prints as much RNA as needed when needed. The print (mRNA) is used to synthesize proteins in the cell and then degraded.

The combination of these two hardware components determines the flow of information in the cell. DNA stores information → RNA is printed on demand → RNA is used as a template to synthesize proteins → proteins perform cellular functions. This is the picture that later became known as the “central dogma of molecular biology.”

In the language of CS, the correspondence is as follows: hard drive (DNA) → printer (RNA polymerase) → executable file (mRNA) → running program (protein). Each stage has a separate hardware component, and each hardware component is specialized for its role. This separation is the key to system stability. Even if the executable file is corrupted, the original source code (hard drive) remains intact. Similarly, even if mRNA is modified, the original genes in DNA are protected.

The Legacy That Continues Today

There are several ways in which the discoveries of Kornberg and Ochoa continue to this day.

PCR (Polymerase Chain Reaction): This method, developed by Kary Mullis in 1983, uses DNA polymerase in a test tube repeatedly to amplify specific DNA fragments by millions of times. Today, it is the foundation of genetic testing, forensic science, and infectious disease diagnosis (COVID PCR). It is a direct descendant of the experimental principle of DNA synthesis in a test tube established by Kornberg.

mRNA vaccines: Since 2020, mRNA vaccines have become world-famous, and the technology has been widely used. In fact, the technology of synthesizing large amounts of mRNA with the desired sequence in a test tube is a descendant of Ochoa’s discovery. Today’s mRNA vaccine production is a process of using RNA polymerase to print large amounts of mRNA from a template DNA in a test tube.

General genetic engineering: DNA recombination, gene cloning, and CRISPR systems all rely on the premise that DNA can be manipulated in a test tube. The experimental basis for this premise was Kornberg’s 1956 experiment.

Why It Matters

What Kornberg and Ochoa left behind was the moment when humanity first held in its hands the “hardware of the life’s information processing system.”

If the DNA double helix revealed the storage format of information, then Kornberg and Ochoa discovered the actual machines that copy and print that information. By demonstrating that these machines function in a test tube, they made it possible for humanity to recreate life’s information processing in the laboratory. This ability became the foundation for molecular biology experimental systems for the next half-century.

In terms of CS, the same principle applies. When you understand both the information storage format and the processing hardware, the system becomes manipulable. If you understand how a compiler works, you can optimize the code, and if you understand how a file system works, you can diagnose performance problems. The combination of abstract understanding and concrete hardware understanding is the key to system manipulation, a principle that is common to both worlds.

The Nobel Committee awarded the prize to these two scientists only six years after the publication of the DNA double helix. This was a very quick recognition, which means that the practical importance of these discoveries was already clear in the scientific community. A good tool is itself the mother of subsequent discoveries, and this is what the award recognized.

1959 Ochoa and Kornberg Summary: Ochoa demonstrated RNA synthesis in a test tube using polynucleotide phosphorylase and provided the experimental basis for decoding the genetic code. Kornberg isolated DNA polymerase from E. coli and established DNA synthesis in a test tube. These are the experimental roots of today’s PCR, mRNA vaccines, and general genetic engineering.

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