The Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race

While DNA protects the genetic information it encodes, it stays at its home in the nucleus of living cells. It is RNA that travels out of the cell to do important work, such as making proteins. At the time of the Human Genome Project, it was believed that RNA’s main job was to carry out the instructions of the DNA, hence the commonly used term “messenger-RNA” (m-RNA). A segment of DNA encoding a gene is transcribed into a snippet of RNA, which travels to the cell’s manufacturing site and enables amino acids to assemble in a specific sequence to make a specific protein. One of the most fascinating proteins RNA helps make are enzymes, which serve as catalysts of biology. Francis Crick called the process of genetic information moving from DNA to RNA to build proteins the “central dogma” of life, a term he later reconsidered.

However, as early as the 1980s, Thomas Cech and Sidney Altman independently discovered that some forms of RNA could also function as enzymes (a departure from the idea that RNA’s only role was to carry out DNA’s instructions). While studying introns, or sequences of DNA (and RNA) that do not contain coded genetic information, Cech and Altman found that some RNA molecules—which they dubbed “ribozymes”—could split themselves, causing a chemical reaction. Typically, clogging introns need to be cut out of RNA by enzymes and the RNA pasted back. However, Cech and Altman found that certain RNA molecules were self-splicing, or performing the cut-and-paste job themselves.

In 1986, Doudna decided to conduct her doctoral research under Szostak, whose focus had shifted from the DNA of yeast to its RNA. Szostak wanted to see if ribozymes could do more than self-splice: Could they replicate themselves? Doudna immersed herself in working on RNA, a risky move at a time when DNA was the toast of the scientific community. Yet Szostak and Doudna knew that if they could figure out the structure of the RNA molecule, then they could perhaps answer the grandest question of science: How did life begin?

Biological principles dictate that life began when DNA, RNA, and proteins combined together. However, it is unlikely that all three molecules originated from “the primordial stew” at the same time. If RNA could be shown to replicate itself, it could be argued that RNA was the original molecule of life. Szostak and Doudna began to unravel how RNA replicated by engineering a self-splicing ribozyme. When the findings were published in Nature in 1989, Doudna began to be recognized as a rising star in the world of biology. But Doudna wanted to explore RNA even further, to understand its molecular structure, a project that was considered almost impossible.

To understand how some RNA replicated itself, Doudna realized she needed to learn structural biology. For her postdoctoral work, Doudna partnered with one of the scientists who had won the Nobel Prize for discovering ribozymes: Thomas Cech of the University of Colorado, Boulder. In Colorado, Cech was using X-ray crystallography to study RNA the same way Rosalind Franklin had studied DNA. Doudna’s move to Boulder was also prompted by her recent marriage to Harvard medical student Tom Griffin. Griffin, who was from a military family, loved Colorado. However, owing to their differing interests, the couple separated a few years after the move.

At Cech’s lab, Doudna figured out that if she determined the three-dimensional structure of the intron, she could see how its twists and folds brought the right atoms together to catalyze the snippet of RNA to replicate itself. Doudna started with crystallizing RNA, with the help of graduate student Jamie Cate. A serendipitous lab accident involving an overheated incubator revealed RNA could in fact crystallize at higher temperatures. Though Doudna began to achieve good crystals, they often broke down under X-ray. Tom Steitz, a Yale biochemist visiting Boulder, suggested to Cate that they cryocool the crystals in liquid nitrogen (which freezes matter very fast) so their structure would be preserved even under X-ray. Soon, Doudna had enough high-quality crystals for her to eventually learn RNA’s structure. Impressed by Steitz’s lab, Doudna accepted a tenure-track position at Yale after finishing her postdoctoral work in 1993. Cate transferred to Yale so he could continue working with Doudna.

Though the crystals Doudna and Cate had achieved diffracted X-rays well, the duo were hit by another roadblock: the “phase problem,” as it is known in crystallography parlance. X-ray detectors can measure the intensity of a wave, but not its phase or location within a wave cycle. One way to tackle the problem is to introduce metal ions in the crystal. Since X-rays can map metal, they can pinpoint the location of the wave and use it to calculate the rest of the molecular structure. The metal-ion method had never been tried successfully with RNA. Cate solved the problem by using osmium hexamine, a molecule that has an affinity for interacting with nooks of RNA. Consequently, Cate and Doudna were able to achieve an electron density map that would provide vital clues about the structure of an important portion of the RNA they were studying.

While Doudna was coming closer to the answer of RNA’s structure, her father Martin was fading from metastatic cancer. Doudna spent the fall of 1995 flying between New Haven and Hilo to spend time with her father, and she found that discussing her work with him helped clarify her ideas about what the data meant. When Martin died a few months later, his passing coincided with Doudna’s first major scientific achievement. Doudna, Cate, and their team had successfully determined the location of every atom in a self-splicing RNA molecule. A specific area in the molecule enabled RNA to pack helices together and create its three-dimensional shape. What was special to this area? Doudna and her team showed that a cluster of metal ions in that domain formed a core around which the structure folded. In a prescient statement about her celebrated discovery, Doudna said that one of the possibilities of knowing RNA was an ability to treat people with genetic defects.

Doudna and Cate’s collaboration soon grew into a romantic partnership. The two married in Hilo in summer 2000; their only child, Andrew, was born two years later. Since the family wanted to be in the same location, Doudna accepted a job offer from the University of California, Berkeley. There, Doudna became interested in how the RNA in some viruses, such as coronaviruses, enabled them to hijack a cell’s protein-building machinery.

In fall 2002, during Doudna’s first semester at Berkeley, there was a deadly coronavirus outbreak in China. The virus was named Severe Acute Respiratory Syndrome (SARS)-CoV. In 2020, with the emergence of another infectious coronavirus, it would be renamed SARS-CoV 1.

Doudna’s other interest at Berkeley became a phenomenon known as RNA interference. Normally, genes encoded in DNA send messenger-RNAs to direct the building of proteins. However, certain small molecules intercept and corrupt the RNA. RNA interference works by deploying an enzyme known as “Dicer,” which snips a strip of RNA into fragments. These small fragments or molecules seek out a messenger RNA with matching letters and use a scissor-like enzyme to slice and silence it. Through X-ray crystallography, Doudna learned that Dicer acts like a ruler, with a clamp at one end to grab an RNA and a cleaver at the other to slice the segment at the correct length. Doudna and her team also showed how Dicer could be reengineered to “silence other genes.” In other words, RNA interference could have potential uses in treating genetic conditions. Additionally, RNA interference can be potentially utilized to fight viruses. Organisms other than humans do deploy RNA interference to fight off viruses. Researchers hope that drugs based on RNA interference may someday be used to treat severe viral infections in humans, like SARS-Cov-2. Doudna’s findings on Dicer were published in Science in 2006. A few months later, a scientist from Spain published a paper on another virus-fighting mechanism as seen in micro-organisms, such as bacteria. At first, it was assumed this mechanism also worked through RNA interference. However, the phenomenon would turn out to be different.