Putting DNA to Work as a Biomedical Tool
Jacqueline Barton is on intimate terms with DNA, the master molecule of life. She knows its secret crevices, weird loops, strange digressions and switchbacks. When she talks about DNA, her hands trace its imaginary contours, lovingly, like a sculpture. They slice through the air, showing how the “steps” in the DNA ladder stack up on each other like a pile of coins.
She pokes at a huge plastic DNA model in her office to show how it jiggles, probes it like a doctor palpating a patient. Her fingers follow an imaginary electron moving through the strand.
She also gets her hands on the real thing, working amazing tricks on the spiraling double-helix that encodes all the genetic instructions for life.
The chemist churns it out in her Caltech lab, tailor-made, one link at a time. She fits it out with fancy metallic propeller blades that slide into its creases like tongues. She dresses it up in fluorescent lights, like a Christmas tree--each glow signaling a specific “word” in the genetic instructions. She attaches molecular-sized alligator clips to the ends of a DNA chain, moving electrons from one end to another like a current.
There’s a purpose to this play. Barton wants to use her inventions for medicinal purposes, as made-to-order molecules that could kill viruses and perhaps someday prevent, or even cure, cancer.
“DNA-based pharmaceuticals,” she calls them.
While other researchers manipulate DNA to alter genes or kill cancer, her pioneering approach relies on tiny metal-based molecular machines of her own design--machines that have the potential to change the way scientists approach this all-important molecule.
Radiation’s Effect on DNA
Her most recent and controversial work has focused on trying to find out what happens when DNA gets damaged by radiation from the sun, or gamma rays from outer space--something that happens every day. Does the radiation do damage at the spot where it strikes, like lightning striking an open field? Or does the damage somehow travel down the DNA strand to a specific, most sensitive, site--like lightning traveling down a telephone pole and into a house?
Her tentative answer is yes, it can travel.
If she’s right, the finding might lead to methods for targeting dangerous bits of dividing cancer cells for destruction.
“It would be like the remote control on your TV,” she says. “You do something from a distance, but you still have a measure of control over what you’re doing.”
This concept has not been popular with many researchers who haven’t traditionally believed that electrons could travel easily from one spot on DNA to another. What’s more, they think Barton is stepping dangerously over disciplinary lines. After all, she’s an inorganic chemist, a specialist in metals assumed to have little to do with life.
“I probably didn’t realize what a crazy idea this was [to some other scientists],” she says.
It’s a radically different way to think about DNA. As a chemist, Barton is interested in the architectural structure of the master molecule. She studies its properties--like electrical conductivity--as if it were an inorganic crystal, such as a piece of a rock or a semiconductor in a cell phone.
Like many scientists, she’s taken some flak for going against the grain. But risks are part of the bargain, she says, and she takes criticism in stride.
“When you rattle the foundations, people get nervous,” she says. “But at places like Caltech, it’s OK to go out on a limb. It’s OK to have an idea proved wrong. I’m supposed to be pushing the boundaries.”
Her work has earned an impressive array of awards. She was the first woman to win the prestigious Nichols medal (14 winners have gone on to win the Nobel Prize), the first woman to win the National Science Foundation’s Waterman Prize (known as the junior Nobel Prize), and the first woman given a chair--the Hanische Chair--at Caltech. She also has won a MacArthur Fellowship--the so-called “genius” award.
An Intricate 3-D Structure
Composed of billions of atoms, DNA looks something like a twisted ladder, with two outside rails connected by a series of molecular links. The various links are letters in the alphabet that spell out genetic instructions for a cell.
But unlike steps in a ladder, the links can slide around, like a “stack of copper pennies,” as Barton calls them. The steps can twist up or down, instead of lying flat. The rails don’t always run smoothly, but bulge and loop in shapes essential to correctly conveying instructions to other parts of the cell.
“These weird shapes in DNA . . . are places where things get turned on and off,” she says. They are, in effect, bits of code that tell biological reactions to start and stop. Because of DNA’s intricate three-dimensional structure, she designs three-dimensional tools to work with the molecule. “I’m always thinking about 3-D structure,” she says.
Barton’s lab comprises a veritable DNA world, a factory for making molecular gadgets that attach to the twists in the spiral chain and set off tiny molecular-sized “bombs” or switch on molecular lights that glow in the dark.
The several dozen rooms are thick with that strong chem-lab smell, stacked with jars of strange, dark fluids, glowing mixtures in glassware and radioactivity warning signs. Dozens of graduate and post-doctoral students sit at lab benches and computers, adding small drops of liquid to miniature test tubes or peering into various machines. A nuclear magnetic resonance machine maps the protons in the DNA, while other machines measure whether the molecules spiral to the left or right. “I get to do all this, and I don’t have to clean anything,” she says. (Her students take care of that.)
One of her proudest possessions is the “DNA machine,” a microwave oven-sized stack of four bottles attached to a computer. Each bottle holds one of the four basic ingredients of DNA, known by their chemical initials A,C,G,T. One atom at a time, the machine adds ingredients to make DNA to order. “You punch in a sequence,” she says, “it churns it out.”
Making pure, precise DNA is essential for her experiments. Natural DNA is inconsistent, which blurs experimental results. “The structures are all a little bit different,” she says. “So you don’t know what you’ve got.”
When Barton got interested in DNA-based drug therapy, she immediately realized that metals could be useful building blocks. Most of her complexes are built around the metals rhodium and ruthenium. The relatively heavy atoms of these elements make a stable skeleton for her homemade structures.
Moreover, the loose electrons hovering in the outer shells of the atoms easily form attachments with other atoms. Both rhodium and ruthenium are surrounded by six sites where electrons can easily interact--electrical glue points that make them ideal as atomic-size building blocks. The metals make a perfect core for the propeller blades, or anchors for the light switches she uses to probe DNA.
Utilizing a Metal That Glows
And contrary to conventional wisdom, metals are not total strangers to life. Over the past decade, it has become increasingly clear that metals like zinc and iron play a critical role in living organisms, even though they are present only in trace amounts. And some metals change color when their surroundings change, making them useful biological probes.
“Why is blood red?” asks Barton. “Because the iron in it is red when it carries oxygen. When it’s not carrying oxygen [when it’s returning to the heart after depositing oxygen in the cells], it’s bluish.”
She takes this a step further, using metals where they don’t belong. Ruthenium, for example, isn’t found in living things. But it can glow. “It glows like Day-Glo,” she says. “That makes it a wonderfully powerful tool. These are the tools of the trade.”
Her molecular light switch, like all the other metal complexes made in her lab, starts with a metal atom, decorated with carbons and hydrogens typical of organic molecules. Fashioned into a shape somewhat like propeller blades--with “arms” sticking out at twisted angles--the complex fits into the curves of DNA at a predesignated site.
One of the propeller blades is extra long, like a tongue, and slips inside the rungs of the DNA ladder. When it is nestled inside, it glows, signaling its exact location, like a lighthouse on the shore.
Another complex, based on rhodium, breaks a specific spot in the DNA instead of lighting it up. “If I shine [ultraviolet] light on it, it’s like a bomb going off,” she says. “It breaks the DNA backbone.”
The metal complexes are completely unnatural molecules. Conceivably, they could be used some day to target sites on the DNA chain for delivery of anti-cancer agents or other drugs, or cutting the bonds that hold DNA together, or locating genes.
“Say you make an anti-HIV drug and you want to get it to bind to a certain spot on the DNA [to stop cell division, for example],” Barton says. “So you take your drug, you attach a light switch. Then when it snuggles up in the DNA, when it’s safe, it lights up. It’s a good tracer. And it’s nonradioactive.”
‘Like a Mosquito Moving an Elephant’
Lately, Barton has been investigating how electrons travel through DNA in order to better understand how damage to one spot on the DNA helix might travel to another, more biologically sensitive spot and cause cancer. Although electrons are infinitesimally tiny bits of electrical fluff compared to the nuclear cores of atoms, they do virtually all of the chemistry: The electrons determine which atoms stick together and what molecules get made.
“It’s like a mosquito moving an elephant,” Barton says. The shuffling around of electrons is behind every living breath and thought, every bit of sunlight that gets converted into food inside the green leaf of a plant, every bottle of fine wine. “The simplest chemical reaction is an electron moving from one atom to another,” she says.
When ultraviolet light from the sun shines on skin cells, for example, they can knock out electrons, or insert electrons in the “wrong” place, eventually causing cancer. The question is: Do the extra electrons stay put wherever they hit, doing damage at random? Or do they somehow get siphoned to the most sensitive spots on the DNA chain? If so, does the radiation have a more deadly effect?
“Until now, people have thought it was random,” she says. But her recent experiments suggest electrons can travel--and rapidly--from one spot on the chain to another.
The first experiment suggesting she was right about electron travel through DNA amounted to a kind of DNA battery, with a rhodium complex on one end of the chain and a ruthenium complex at the other. When she built it three years ago, a current appeared to flow rapidly from one end to the other, like a wire.
Wire is only a metaphor, she is quick to point out. The DNA couldn’t be exactly like a wire because unlike the strongly linked copper atoms in a wire, the steps of the ladder are only weakly connected, and slide about. “They’re moving. They’re interacting,” she says.
Yet somehow, an electric charge manages to move from one site on the DNA ladder to another. “We know that it works,” Barton says. “We don’t know how it works. What’s new and unprecedented is that it occurs at long range. It’s action at a distance.”
Her most recent work, appearing in the journals Science and Nature, seems to have made her case for electron travel through DNA even stronger. In one experiment, she zapped a strand of tailor-made DNA to deliberately inflict the kind of damage normally produced by overexposure to cancer-causing ultra-violet radiation. Then, in a subsequent experiment, she repaired the damage using visible light.
Both damage and repair involved adding or subtracting an electron.
The key was that the healing light wasn’t shined on the actual site of the damage, but at the other end of the strand. The electron traveled from one end of the DNA to the other.
To further prove the point that the electron actually traveled down the helix, she stuck a little bulge in the DNA ladder, by adding a few extra steps. If the electron really traveled down the steps of the ladder, then the bulge should be an obstacle, and the flow should stop. It did.
‘Willing to Ask Very Stupid Questions’
All this tells her that DNA is not like protein; it has an inherently different structure, and scientists need to do a lot more work before they understand how electrons flow through this master molecule of life. That understanding, in turn, will be critically important to unraveling the mystery of just how DNA gets damaged, and how that damage gets transferred to different locations.
Whether Barton’s marriage of metals and DNA leads to useful biomedical tools won’t be clear for a long time. Meanwhile, she says she’ll continue to stick her nose in subjects where, technically, she doesn’t belong.
But ignorance, she says, can be extremely helpful. “You have to be willing to ask very stupid questions.”
Ultimately, she knows that risk is a necessary part of science, and breaking new ground--right or wrong--always leads to a certain amount of skepticism. “Scientists are very conservative,” she says. “People are always trying to prove you wrong, so you can’t be married to your point of view, because you’re always testing it.”
“I’m always scared,” she says. “But one has to try. People may think you’re wrong. But the opportunity to learn is fantastic.”
