All Shook Up: Researchers Mix RNA and DNA to Study How Life’s Process Began Billions of Years Ago

RNA and DNA

For decades, chemists have tested theories for how life began on Earth. One hypothesis has caught the scientific imagination for years: RNA World. This theory proposes that prebiotic molecules joined up early on to form RNA, the molecules that carry instructions from DNA in organisms today. RNA World posits that once RNA formed on Earth, it began replicating itself and later gave rise to molecules like DNA.

RNA World is a fascinating theory, says Ramanarayanan Krishnamurthy, PhD, an associate professor of chemistry at Scripps Research, but it may not hold true. The problem is that the ingredients, such as enzymes, to make RNA World work just didn’t exist on early Earth.

“RNA World has given rise to the idea that if you somehow synthesize RNA, which can replicate and catalyze reactions, everything else automatically follows,” says Krishnamurthy, who is a member of the Simons Collaboration on the Origins of Life and holds a joint appointment with the Center for Chemical Evolution, co-funded by the NASA Astrobiology program and the National Science Foundation. “That’s not the case, because RNA World relies on RNA replicating itself, which is very difficult.”

Part of the challenge is that RNA molecules form stable structures called duplexes. These structures have what’s known as a strong binding affinity. This means the RNA molecules have difficulty separating from each other and acting as templates for replicating further in the absence of enzymes.

Krishnamurthy now has experimental evidence to demonstrate that life’s process on Earth could have actually started with molecules that looked like a mixture of RNA and DNA. In the latest issue of Nature Chemistry, he and the study’s first author, Subhendu Bhowmik, PhD, also of Scripps Research, report that these mixed molecules form unstable duplexes and have lesser affinity for themselves. Surprisingly, these “chimeras” have stronger affinity for RNA and DNA, which allows them to act as templates for making RNA or DNA.

In fact, the researchers were able to form these chimeras under lab conditions and show that they have the potential to replicate RNA and DNA, and the thus formed RNA and DNA are able to reproduce the chimeras. This behavior could lead to a cross-catalytic amplification of RNA and DNA—a key step toward the evolution of complex organisms.

“A provocative implication of this study is that RNA and DNA could have appeared simultaneously instead of the widely accepted RNA World theory, where RNA appears first and then gives rise to DNA,” says Krishnamurthy. “This means mixtures of RNA and DNA could have co-existed.”

In organisms today, DNA and RNA perform very different roles in our cells. The new project experimentally supports the idea that life could have arisen from a much messier system, where “pure” RNA and DNA did not exist yet. As Krishnamurthy says: “It’s OK not to have clean chemistry.”

In work spearheaded by Bhowmik, a research associate in Krishnamurthy’s Scripps Research laboratory, the team also created “heterogeneous” mixed molecules made of RNA and a synthetic molecule called TNA, which has been proposed to be a plausible ancestor of RNA (“pre-RNA”). TNA is very similar to RNA, but scientists have replaced one type of sugar molecule (ribose) with another (threose). This allows TNA to cross-pair with RNA and DNA. Krishnamurthy and Bhowmik say a molecule like TNA could have performed this cross-pairing at the very beginning of evolution, leading to the side-by-side formation of TNA and RNA.

By mixing RNA-DNA, the researchers showed that it could have been possible to form a mixed molecule that could work as templates for RNA and DNA. This mixed molecule is also a high-energy system in the sense that it forms unstable duplexes. The new research shows that these unstable duplexes (higher energy systems) are capable of giving rise to RNA and DNA, which form more stable duplexes (lower energy systems). Thus, there is a thermodynamically favorable movement from chimeric systems (less-stable, higher-energy) to homogeneous systems (more-stable, lower-energy).

“Hybrid system like these could have helped in the evolution of homogeneous systems,” says Bhowmik.

We’ll never know exactly how early life formed, but the experiments at least show chemical reactions that could have eventually led to the pure RNA and DNA sequences that support life today. The work also supports the findings of a 2018 Scripps Research study, which showed how an engineered bacterium can function with a mixed RNA-DNA genome.

Krishnamurthy says research going forward should focus on which ingredients needed for RNA-DNA chimeras would have been available on prebiotic Earth. The scientists used several molecules that were likely not available back then, though similar ingredients should have existed. The new study gives researchers a “proof of principle” that these reactions can work, and Krishnamurthy plans to follow up with further experiments to explore the pathways for how life’s molecules could have come together. “This study is the first step in that direction,” he says.

Krishnamurthy is also interested in how RNA-DNA chimeras might be used in medicinal chemistry studies. He says these mixed systems may help researchers overcome some challenges in genetic sequencing.

The study, “The role of sugar-backbone heterogeneity and chimeras in the simultaneous emergence of RNA and DNA,” was supported by NASA (grant NNX14AP59G), the Simons Foundation (grant 327124) and a NASA Astrobiology Postdoctoral Program fellowship.