Stanford scientists have synthesized a molecule of DNA that is capable of shutting off specific genes in living bacteria. Dubbed the "nanocircle," the new nanometer-size molecule might one day give researchers the ability to target harmful genes that cause cancer and other diseases in humans.

"In the long range, we hope that nanocircles could be used for genetic therapy in people," said Eric T. Kool, a professor of chemistry at Stanford who led the nanocircle study. The results were published in the Jan. 8 issue of the Proceedings of the National Academy of Sciences (PNAS) in a paper co-authored by Kool, former postdoctoral fellow Tatsuo Ohmichi and graduate student Angéle Maki.

Eric T. Kool is the professor of chemistry who led the nanocircle study. Photo: L.A. Cicero

Rolling circles

Kool helped pioneer nanocircle technology in 1991 while at the University of Rochester, where he synthesized the first circular DNA molecules capable of replicating themselves in a test tube when combined with special DNA-copying enzymes and other chemicals.

The technique -- known as "rolling circle amplification" -- is now one of the hottest fields in biotechnology, because it offers the potential to produce and detect more copies of a specific DNA sequence faster and cheaper than other methods.

"What is new about the PNAS study is that, for the first time, we used a nanocircle in a living cell -- the bacterium E. coli," Kool noted.

He and his colleagues wanted to see if a synthetic molecule of circular DNA could target a specific gene in E.coli. To do that, they needed to design a DNA nanocircle that could duplicate large numbers of ribozymes -- enzymes found in all living cells that are capable of altering the function of individual genes in the organism's DNA. Ribozymes are made of RNA -- protein-producing molecules manufactured by genes.

"Ribozymes are biologically active," Kool said. "They can inhibit or shut down a gene by destroying its RNA."

In nature, ribozymes are assembled by DNA molecules, which act as templates. First, the DNA binds with an enzyme called RNA polymerase, then the ribozyme is formed. The challenge for researchers was to figure out which synthetic nanocircle was best suited for binding with the naturally existing RNA polymerase in the bacterial cell.

"RNA polymerases are picky, so the real trick was making a nanocircle that was especially good," Kool noted. "We said, 'Let's let the RNA circles tell us which polymerase they like best -- let them tell us who the winner is, and then we'll know which circle is best.'"

The researchers ended up making 15 generations of nanocircles until they finally came up with the best DNA sequence.

"It was evolution in a test tube," Kool recalled.

The chosen nanocircles were then added to the E. coli to determine if the mixture would produce ribozymes capable of cleaving a specific drug-resistant gene in the bacteria. The results were clear: The targeted gene stopped functioning more than 90 percent of the time.

Trojan horse

"Our study demonstrated that nanocircles can act like a Trojan horse," Kool said. "They enter cells and start producing ribozymes that can be targeted against a particular gene. But the nanocircle itself does not replicate itself and eventually leaves the cell."

This is a chemical model of a DNA nanocircle synthesized in the laboratory of Professor Eric Kool. When inserted into a bacterial cell, the nanocircle acts like a Trojan horse, producing RNA in the cell that shuts specific, disease-causing genes. Credit: Eric Kool

Kool's goal is to create nanocircles that can inhibit disease-causing and mutant genes in people that could be used to treat a variety of illnesses from AIDS to cancer. As a first step, his lab is developing nanocircles that will shut down genes in tiny worms called nematodes.

"We also would like to see if we can use nanocircles to eliminate a harmful bacterium or virus by shutting down an essential gene inside the organism itself -- a true Trojan horse," Kool added.

He also noted that nanocircle technology could prove less expensive than making ribozymes directly and adding them to cells -- because relatively small numbers of nanocircles can produce thousands of ribozymes.

The PNAS study was funded by the U.S. Department of Defense Breast Cancer Research Program, administered by the US Army.

These atomic force microscopy images (obtained with collaborators at UC-Santa Barbara) show actual strands of RNA (yellow) that were produced from nanocircles in E. coli bacteria. The nanocircles - too small to see - are located inside RNA polymerase enzymes, which appear as white blobs. Credit: Eric Kool

• Kool Group website
  
  
• Proceedings of the National Academy of Sciences website