In her laboratory at the University of Illinois at Urbana-Champaign, Maria Spies gets right down to the level of single molecules to understand the workings of DNA helicases—motor enzymes in the cell that convert chemical energy into mechanical work. The helicases she studies "unzip" DNA so it can be repaired or plow away obstacles that obstruct the progress of various DNA maintenance machineries. When these critical proteins "run off the rails," cells become weaker and more vulnerable to cancer, premature aging, and ultra-sensitivity to sunlight.
Spies's fascination with biology and things mechanical was cemented as a postdoctoral researcher at the University of California, Davis. Using an ingenious blend of lasers, fluorescent markers, and advanced microscopy techniques, she was able to spy on a single bacterial helicase, RecBCD, as it zoomed along a stretch of DNA, scanning for locations in the genome that needed its attention.
"There is a specific hot spot in DNA that this enzyme recognizes," she says. Though it's not clear how that recognition occurs, Spies's experiments showed what happens next: When RecBCD binds to the DNA sequence, the enzyme reorganizes its motor subunits and changes speed, switching from a "fast motor" to a "slow" one.
The unexpected discovery of the "bipolar motor" is changing the way scientists look at these enzymes and how they function.
"This helicase is an amazing molecular machine," Spies says. And she should know. Her experience with machines extends back to her undergraduate studies in her native Russia, where she enrolled in an engineering program focused on industrial robots design.
"After about a year in the program I realized I was more interested in living things, so biophysics was a good option," she says. "I could still look at machines, but they are biological machines."
Studies carried out by Spies's lab hint at how human DNA repair helicases work by themselves and, more importantly, as components of complex genome maintenance machines. "Often, malfunctions in DNA repair are associated with cancer and aging," she notes. At the same time, certain cancer cells can regain the ability to fix errors in DNA, making them resistant to chemotherapy, radiation, or both.
"If we understand how those DNA repair machines work, we might be able to design the perfect monkey wrench" to eliminate cancer's resistance to treatment, she says.
Spies is also focused on a group of proteins involved in homologous recombination, the shuffling of genetic material between two strands of DNA. One such protein, Rad52, is used by some cancer cells as part of a DNA-repair pathway, making them resistant to treatment. Normal cells have other ways to repair DNA, so a drug that stops Rad52's function should have minimal toxicity for normal cells and also reduce the chances for the tumor cells to acquire resistance. Spies's lab uses fluorescence-based techniques to watch Rad52 proteins performing different tasks on DNA. Her team's effort to understand the specific steps the protein takes to manipulate DNA will help in the search for drugs that interfere with all or some of its functions.
Spies is also studying a group of iron-containing helicases. One of these helicases, called XPD, grabs DNA in a very precise manner and unwinds it so that the damage can be cleared and replaced with a "healthy" DNA strand. Mutations in XPD have been linked with several human diseases, including xeroderma pigmentosum and Cockayne syndrome, rare disorders marked by DNA damage, sensitivity to sunlight, and premature aging.
The XPD protein has an iron-sulfur cluster at its core, which Spies is using as a molecular beacon to help her keep track of XPD's movements. The iron quenches the fluorescence of many dyes, so Spies can label a DNA molecule with fluorescent dye, "release" the helicase to do its job, and follow its progress via change in the fluorescence of the reporter dye. Using this technique, she can pinpoint location of the helicase on DNA as it moves along and navigates a complex molecular traffic jam.
She has also invented a technique that allows her to track multiple molecules with fluorescent markers to see how they interact. Using this approach, Spies has identified a protein that helps a form of XPD found in archaea, which is similar to one found in humans, unwind DNA.
As to the future, "there are still so many questions to be answered," she says. "I think I've found my niche."