Enlarge / The Manu area of Peru contains a number of ecological zones. (credit: Corey Spruit / Wikimedia Commons )

Peru’s Manu Biosphere Reserve is the largest rainforest reserve in the world and one of the most biodiverse spots on the planet. Manu is a UNESCO-protected area the size of Connecticut and Delaware combined, covering an area where the Amazon River Basin meets the Andes Mountain Range. This combination forms a series of unique ecosystems, where species unknown to science are discovered every year. The remoteness of the region has helped preserve its biodiversity but adds to the challenges faced by the scientists who are drawn to study it.

Trapping wildlife for research in the dense jungle is impractical, especially considering the great distances researchers have to travel within Manu, either through the forest or on the waterways. It’s an expensive proposition that inevitably exposes the trapped animals to some amount of risk. Trapping rare and endangered animals is even more difficult and comes with significant risks to the animal .

Trapping beetles, however, does not pose the same challenges. They’re easy to catch, easy to transport, and, most importantly, carry the DNA of many animals in and on them. Any animal a biologist could hope to study leaves tracks and droppings in the forest, and the beetles make a living by cleaning that stuff up.

Enlarge / Drawing of a trade expedition to Punt during the reign of Queen Hatshepsut. Note the presence of baboons on board the lower ship. (credit: Nastasic )

One of the most enduring mysteries within archaeology revolves around the identity of Punt, an otherworldly “land of plenty” revered by the ancient Egyptians. Punt had it all—fragrant myrrh and frankincense, precious electrum (a mixed alloy of gold and silver) and malachite, and coveted leopard skins, among other exotic luxury goods.

Despite being a trading partner for over a millennium, the ancient Egyptians never disclosed Punt’s exact whereabouts except for vague descriptions of voyages along what’s now the Red Sea. That could mean anywhere from southern Sudan to Somalia and even Yemen.

Now, according to a recent paper published in the journal eLife, Punt may have been the same as another legendary port city in modern-day Eritrea, known as Adulis by the Romans. The conclusion comes from a genetic analysis of a baboon that was mummified during ancient Egypt’s Late Period (around 800 and 500 BCE). The genetics indicate the animal originated close to where Adulis would be known to come into existence centuries later.

Enlarge (credit: NIH )

Every person starts as just one fertilized egg. By adulthood, that single cell has turned into roughly 37 trillion cells, many of which keep dividing to create the same amount of fresh human cells every few months.

But those cells have a formidable challenge. The average dividing cell must copy—perfectly—3.2 billion base pairs of DNA, about once every 24 hours. The cell’s replication machinery does an amazing job of this, copying genetic material at a lickety-split pace of some 50 base pairs per second.

Still, that’s much too slow to duplicate the entirety of the human genome . If the cell’s copying machinery started at the tip of each of the 46 chromosomes at the same time, it would finish the longest chromosome—No. 1, at 249 million base pairs—in about two months.

“The way cells get around this, of course, is that they start replication in multiple spots,” says James Berger, a structural biologist at the Johns Hopkins University School of Medicine in Baltimore, who co-authored an article on DNA replication in eukaryotes in the 2021 Annual Review of Biochemistry. Yeast cells have hundreds of potential replication origins, as they’re called, and animals like mice and people have tens of thousands of them, sprinkled throughout their genomes.

“But that poses its own challenge,” says Berger, “which is, how do you know where to start, and how do you time everything?” Without precision control, some DNA might get copied twice, causing cellular pandemonium.

Keeping tight reins on the kickoff of DNA replication is particularly important to avoid that pandemonium. Today, researchers are making steps toward a full understanding of the molecular checks and balances that have evolved in order to ensure that each origin initiates DNA copying once and only once, to produce precisely one complete new genome.

Do it right, do it fast

Bad things can happen if replication doesn’t start correctly. For DNA to be copied, the DNA double helix must open up, and the resulting single strands—each of which serves as a template for building a new, second strand—are vulnerable to breakage. Or the process can get stuck. “You really want to resolve replication quickly,” says John Diffley, a biochemist at the Francis Crick Institute in London. Problems during DNA replication can cause the genome to become disorganized, which is often a key step on the route to cancer.

Some genetic diseases, too, result from problems with DNA replication . For example, Meier-Gorlin syndrome, which involves short stature, small ears, and small or no kneecaps, is caused by mutations in several genes that help to kick off the DNA replication process.

It takes a tightly coordinated dance involving dozens of proteins for the DNA-copying machinery to start replication at the right point in the cell’s life cycle. Researchers have a pretty good idea of which proteins do what, because they’ve managed to make DNA replication happen in cell-free biological mixtures in the lab. They’ve mimicked the first crucial steps in initiation of replication using proteins from yeast —the same kind used to make bread and beer—and they’ve mimicked much of the entire replication process using human versions of replication proteins , too.

The cell controls the start of DNA replication in a two-step process. The whole goal of the process is to control the actions of a crucial enzyme—called a helicase—that unwinds the DNA double helix in preparation for copying it. In the first step, inactive helicases are loaded onto the DNA at the origins, where replication starts. During the second step, the helicases are activated, to unwind the DNA.

Ready (load the helicase) …

Kicking off the process is a cluster of six proteins that sit down at the origins. Called ORC, this cluster is shaped like a double-layer ring with a handy notch that allows it to slide onto the DNA strands, Berger’s team has found.

In baker’s yeast, which is a favorite for scientists studying DNA replication, these start sites are easy to spot: They have a specific, 11- to 17-letter core DNA sequence, rich in adenine and thymine chemical bases. Scientists have watched as ORC grabs onto the DNA and then slides along, scanning for the origin sequence until it finds the right spot.

But in humans and other complex life forms, the start sites aren’t so clearly demarcated, and it’s not quite clear what makes the ORC settle down and grab on, says Alessandro Costa, a structural biologist at the Crick Institute who, with Diffley, wrote about DNA replication initiation in the 2022 Annual Review of Biochemistry. Replication seems more likely to start in places where the genome—normally tightly spooled around proteins called histones—has loosened up.

The initiation of DNA replication starts at the tail end of the previous cell division and continues through the cell cycle phase known as G1. DNA synthesis happens during the S phase. Levels of a protein called CDK are critical to ensuring that DNA is replicated once and only once. When CDK levels are low, helicases can jump onto the DNA and start to unwind it. But repeat binding does not happen because CDK levels rise, and this blocks the helicase from binding again. (credit: Knowable Magazine )

Once ORC has settled onto the DNA, it attracts a second protein complex: one that includes the helicase that will eventually unwind the DNA. Costa and colleagues used electron microscopy to work out how ORC lures in first one helicase, and then another . The helicases are also ring-shaped, and each one opens up to wrap around the double-stranded DNA. Then the two helicases close up again, facing toward each other on the DNA strands, like two beads on a string.

At first, they just sit there, like cars with no gas in the tank. They haven’t been activated yet, and for now the cell goes about its usual business.

Get set (activate the helicase)...

Things kick into high gear when a crucial molecule called CDK waves the green flag, jump-starting chemical steps that lure in even more proteins. One of them is DNA polymerase—what Costa calls the “typewriter” that will build new DNA strands—which hitches onto each helicase. Others activate the helicases, which can now burn energy to chug along the DNA.

As this occurs, the helicases change shape, pushing on one DNA strand and pulling on the other. This creates strain on the weak hydrogen bonds that normally hold the two strands together by the bases—the As, Cs, Ts and Gs that make up the rungs of the DNA ladder. The two strands get ripped apart. Costa and colleagues have observed how the two helicases untwist the DNA between them , and they’ve seen how the helicases keep the unbound bases stable and out of the way.

Left: Several genes involved in the initiation of DNA replication (horizontal axis) are amplified—that is, mistakenly copied in extra numbers — to varying degrees (vertical axis) in different cancers. Right: On chromosome 8, a cluster of three genes—shown in green text—are frequently amplified together in certain cancers. (credit: Knowable Magazine )

Go!

At first, both helicases are wrapped around both strands of DNA, and they can’t get very far like this, because they are facing each other and will just run into each other. But next, they each undergo a change in position, spitting one DNA strand or the other out of the ring. Now separated, they can jostle past each other, and replication proceeds apace.

Each helicase motors along its single strand, in the opposite direction from the other. They leave the origin behind and yank apart those hydrogen-bonded base pairs as they travel. The DNA polymerase is right behind, copying the DNA letters as they’re freed from their partners.

CDK’s second job is to stop any more helicases from hopping on the origins. Thus, there is one start of replication per origin, ensuring proper copying of the genome—although copying doesn’t begin at the same time at each site. The whole process of DNA replication, in human cells, takes about eight hours.

There is still plenty to be worked out. For one thing, the DNA that’s being copied is not a naked double helix. It’s wrapped around histones and attached to lots of other proteins that are busy turning genes on or off or making RNA copies of the genes . How do those jostling proteins affect each other and avoid getting in each other’s way?

Beyond this fascinating, fundamental biology—a remarkable process essential for all life on Earth—there are implications for diseases like cancer. Scientists already know that faulty replication can destabilize DNA, and an unstable genome that’s prone to mutation may be an early hallmark of cancer development. And they are further investigating links between replication proteins and cancer.

“I think that there are opportunities for therapeutic interventions for these systems,” says Berger, “once we have enough insights about how they work and what they look like.”

Amber Dance , a science writer in the Los Angeles area, also likes to break large tasks into smaller segments: It took her five days to complete the steps to draft this article. This article originally appeared in Knowable Magazine , an independent journalistic endeavor from Annual Reviews. Sign up for the newsletter .

Enlarge / People may accidentally sequence your DNA while trying to study something else entirely. (credit: Andriy Onufriyenko )

It used to be that if you wanted to find a DNA sequence in a particular sample, you had to go searching for that specific sequence—you had to fish it out with a hook designed especially to catch it. But no more. DNA sequencing technology has advanced to the point where you can take a sample from almost any environment—a drop of water, an ice core, a scoop of sand or soil, even air—and just see whatever DNA is in there.

This provides a non-invasive way to study wild populations and invasive or endangered species and has been used to monitor for pathogens (SARS-CoV-2, mpox, polio, tuberculosis) in wastewater. But guess who else’s DNA is in those environmental samples? Yup. Ours.

Something identifiable in the air

Liam Whitmore is a zoologist and conservationist who studies green turtles. He and his colleagues realized that having human DNA slip into research samples might be an issue, so they looked to see if they could find any in old water and sand samples they had taken as part of a wildlife and pathogen monitoring study. They did. Then they went intentionally searching for specific human sequences, and, in water, sand, and air samples, they found plenty of genomic regions that could identify a person’s ancestry and susceptibility to several diseases. They didn’t go so far as to identify individuals but noted that someone probably could compare these sequences to public genetic data without too much difficulty.

Enlarge / Illustration of a smallpox (variola) virus. A membrane (transparent) derived from its host cell covers the virus particle. Inside this lies the core (green), which contains the particle's DNA genetic material. The core has a biconcave shape. (credit: Katerya Kon / Science Photo Library via Getty )

In November 2016, virologist David Evans traveled to Geneva for a meeting of a World Health Organization committee on smallpox research. The deadly virus had been declared eradicated 36 years earlier; the only known live samples of smallpox were in the custody of the United States and Russian governments.

Evans, though, had a striking announcement: Months before the meeting, he and a colleague had created a close relative of smallpox virus, effectively from scratch, at their laboratory in Canada. In a subsequent report , the WHO wrote that the team’s method “did not require exceptional biochemical knowledge or skills, significant funds, or significant time.”

Evans disagrees with that characterization: The process “takes a tremendous amount of technical skill,” he told Undark. But certain technologies did make the experiment easier. In particular, Evans and his colleague were able to simply order long stretches of the virus’s DNA in the mail, from GeneArt, a subsidiary of Thermo Fisher Scientific.

Enlarge / An attempt to reconstruct what northern Greenland looked like about 2 million years ago. (credit: Beth Zaiken )

When once-living tissue is preserved in a cold, dry environment, fragments of its DNA can survive for hundreds of thousands of years. In fact, DNA doesn't even have to remain in tissue; we've managed to obtain DNA from the soil of previously inhabited environments. The DNA is damaged and broken into small fragments, but it's sufficient to allow DNA sequencing, telling us about the species that once lived there.

In an astonishing demonstration of how well this can work, researchers have obtained DNA from deposits that preserved in Greenland for roughly 2 million years. The deposits, however, date from a relatively warm period in Greenland's past and reveal the presence of an entire ecosystem that once inhabited the country's north coast.

A different Greenland

Over the last million years or so, the Earth's glacial cycles have had relatively short warm periods that don't reach temperatures sufficient to eliminate the major ice sheets in polar regions. But before this time, the cycles were shorter, the warm periods longer, and there were times the ice sheets underwent major retreats. Estimates are that, around this time, the minimum temperatures in northern Greenland were roughly 10° C higher than they are now.

Enlarge / Illumina says its NovaSeq X machine will get the price of sequencing down to $200 per human genome. (credit: Illumina)

The human genome is made of more than 6 billion letters, and each person has a unique configuration of As, Cs, Gs, and Ts—the molecular building blocks that make up DNA. Determining the sequence of all those letters used to take vast amounts of money, time, and effort. The Human Genome Project took 13 years and thousands of researchers. The final cost: $2.7 billion.

That 1990 project kicked off the age of genomics , helping scientists unravel genetic drivers of cancer and many inherited diseases while spurring the development of at-home DNA tests , among other advances. Next, researchers started sequencing more genomes: from animals, plants, bacteria, and viruses. Ten years ago, it cost about $10,000 for researchers to sequence a human genome . A few years ago, that fell to $1,000. Today, it’s about $600.

Enlarge (credit: Adrienne Bresnahan )

The research community is excited about the potential of DNA to function as long-term archival storage. That's largely because it's extremely dense, chemically stable for tens of thousands of years, and comes in a format we're unlikely to forget how to read. While there has been some interesting progress , efforts have mostly stayed in the research community because of the high costs and extremely slow read and write speeds. These are problems that need to be solved before DNA-based storage can be practical.

So we were surprised to hear that storage giant Seagate had entered into a collaboration with a DNA-based storage company called Catalog. To find out how close the company's technology is to being useful, we talked to Catalog's CEO, Hyunjun Park. Park indicated that Catalog's approach is counterintuitive on two levels: It doesn't store data the way you'd expect, and it isn't focusing on archival storage at all.

A different sort of storage

DNA is a molecule that can be thought of as a linear array of bases, with each base being one of four distinct chemicals: A, T, C, or G. Typically, each base of the DNA molecule is used to hold two bits of information, with the bit values conveyed by the specific base that is present. So A can encode 00, T can encode 01, C can encode 10, and G can encode 11; with this encoding, the molecule AA would store 0000, while AC would store 0010, and so on. We can synthesize DNA molecules hundreds of bases long with high efficiency, and we can add flanking sequences that provide the equivalent of file system information, telling us which part of a chunk of binary data an individual piece of DNA represents.

Enlarge / San Francisco Police Chief Bill Scott answers questions in a meeting with the San Francisco Chronicle editorial board on Tuesday, Feb. 15, 2022. (credit: San Francisco Chronicle/Hearst Newspapers via Getty Images)

San Francisco has been sued by a sexual assault victim in a complaint that describes "the San Francisco Police Department's shocking practice of placing crime victims' DNA into a permanent database without the victims' knowledge or consent."

"Plaintiff Jane Doe, a sexual assault survivor, was re-victimized by this unconstitutional practice," alleged the lawsuit filed Monday in US District Court for the Northern District of California. "In 2016, she provided a DNA sample to the San Francisco Police Department as part of its investigation into her sexual assault. However, she never consented to it to be stored or used for any other purpose. Nevertheless, the Department maintained Plaintiff Doe's DNA in the database for more than six years."

According to the lawsuit, Jane Doe was arrested on burglary charges in 2021 after DNA from a crime scene apparently matched the DNA she provided five years earlier. The charges were eventually dropped.