Evolving Artificial DNA?

Evolving Artificial DNA

A team of University of Florida scientists has for the first time developed an artificial chemical system that can mimic the natural evolutionary process living organisms undergo.

Examples of typical polymer structures. Credit: Molecular Universe

Specifically, the team showed that an artificially created DNA-like molecule containing six gene-building nucleotides – instead of the four found in natural DNA – could support the molecular "photocopying" operation known as polymerase chain reaction. The artificial DNA-like molecule directed the synthesis of copies of itself and then copies of the copies, mimicking the natural process of evolution as it was first outlined by Charles Darwin. A nucleotide is a building block of DNA, or a "letter" in the genetic alphabet used to write the "book" describing our genetic inheritance.

"The potential implications of this in diagnosis and medicine are clear," said Steven Benner, a UF distinguished professor of chemistry and anatomy and cell biology and the lead researcher on the study. "This technology will enhance our ability to detect unwanted genetic material from viruses, bacteria and even biological warfare agents. It will also streamline our ability to detect defects in natural DNA, such as those responsible for cancers and genetic diseases."

Thymine structure – one of the bases found in DNA and not in RNA. Credit: Richard B. Hallick

The announcement, which will appear in this week’s edition of the journal Nucleic Acids Research, provides a key step toward developing an artificial form of life. Scientists have been attempting to get artificial chemical systems that support Darwinian evolution for a decade.

Benner and Michael Sismour, a UF graduate student, built on work done by James Watson and Francis Crick, the Nobel Prize winners who proposed 50 years ago the DNA double helix. Watson and Crick showed that four nucleotides encoded information in the DNA molecule, writing our genetic instructions as a string of letters — G, A, T and C, representing guanine, adenine, thymine and cytosine. These letters form the famous Watson-Crick base pair that holds together the two strands of the double helix. This pairing follows simple rules:A from one strand pairs with T from the other, while G from one strand pairs with C from the other.

A decade ago, at the Swiss Federal Institute of Technology, Benner‘s group showed it was possible to increase the number of nucleotides from four to 12. More turns out to be better in the case of DNA. By adding extra nucleotides the number of pairing rules increase, Benner said. "This increases the ways that DNA can come together, giving the biotechnologist enormously enhanced control over how DNA strands assemble."

This increased control has enabled commercially successful diagnostic assays. Today in the clinic, patients infected with HIV and hepatitis C have the load of viruses in their body monitored by diagnostic tools that exploit Benner’s extra nucleotides. That helps doctors better predict when resistant strains of the virus are likely to emerge in the patient.

DNA molecule
The history of a molecule of DNA is buried in its chemical structure
Credit: UIC

"Our artificial DNA has widespread benefit for patients in diagnostics," Benner said. "But until now, it has been largely passive. It has not been able to copy itself."

In order to create a DNA-like molecule able to reproduce itself, the researchers had to find an enzyme, known as a DNA polymerase, that would hold the GATC building blocks of natural DNA in the positions necessary to create the famous Watson-Crick base pair. They then assembled the correctly paired nucleotides into a strand.

Adding a fifth and sixth nucleotide was not difficult from a chemical perspective. But it was difficult to find a DNA polymerase to accept the unnatural nucleotides, Benner said.

"DNA polymerases have evolved for billions of years to accept the four natural letters in DNA — A, T, C, and G." Benner said. "Coaxing them to accept two new letters, like K and X, was difficult."

Primate evolution tree
An evolution tree of the primate species depicted on the tree. Full image.
Credit: Mark A. Klingler, Carnegie Museum of Natural History

Benner turned to a new technology called "protein engineering," to develop an altered DNA polymerase that would work. Using the changed polymerase, the team was able to "evolve" their artificial DNA through five generations.

As it happens, the UF group’s work was anticipated by science fiction. In an episode of the popular TV show the "X-files," one of the characters finds in a virus a fifth and sixth DNA nucleotide – a new base pair – stating: "What you are looking at exists nowhere in nature. It would have to be, by definition, extraterrestrial,"

Or in Benner‘s lab, it seems.

"Considering how hard we had to work to get Earth polymerases to accept our artificial DNA, we doubt that our artificial DNA would survive for an instant outside of the laboratory on this planet. But a six-letter DNA might support life on other planets, where life started with six letters and is familiar with them. Or even DNA that contains up to 12 letters, which we have shown is possible."

"… some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity etc…", Charles Darwin, on the origins of life in tidal pools

"This is quite a breakthrough", said Christopher Switzer, who began this work in Benner’s laboratory in Switzerland over a decade ago and is now chairman of the department of chemistry at the University of California, Riverside.

"The news is highly exciting", said Joseph Piccirilli, who also began research in this area, and who is now a member of the Howard Hughes Medical Institute at the University of Chicago. "It opens up a new direction at the interface between chemistry and biology."

Steven A. Benner is a member of the NASA Astrobiology Institute (NAI).

Related Web Pages

Planetary Biology– Science mag., Benner, et al.
Defining Life
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Earth’s Oldest Fossils Reverse Course
The Cambrian Explosion: Tooth and Claw
The Three Domains of Life
Advances in our Understanding of Life
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