Temple Times Online Edition
    OCTOBER 14, 2004
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Seeing molecules one at a time

Chemistry professor Robert Stanley (left) and Zhanjia Hou, a postdoctoral researcher in Stanley’s lab, assemble the single-molecule
microscope that was acquired through a $162,000 grant from the National Science Foundation.


The National Science Foundation has awarded chemistry professor Robert Stanley $162,000 to build the University’s first single-molecule microscope. The award is part of a three-year, $450,925 grant Stanley has received from the NSF to explore DNA repair.

“It’s a bit of a misnomer that the single-molecule microscope can image single molecules,” Stanley said. “You don’t actually visualize the single molecule as you would with an electron microscope.”

Stanley said researchers use the fluorescent properties of molecules or attach fluorescent probes on a molecule to observe the way that particular molecule is functioning. The beam from a state-of-the-art ultrafast laser excites the molecule, and the light emitted from that fluorescent species is collected by the microscope’s objective and is separated out from the laser beam.

“That’s the signal that you then observe,” he said.

Stanley and his group will use the microscope to observe how the structure of DNA changes over time or is manipulated.

“People usually think of DNA as a double-helical ladder,” he says. “But in fact, DNA is a very dynamic system. By using the fluorescent probes that mimic the constituent bases of DNA, we can gain valuable information about how DNA is a dynamic system, how it opens and closes, and to what extent that affects its interactions with proteins that manipulate the DNA.

“Without a single-molecule microscope, those experiments would be very, very difficult,” he said.

Stanley is particularly interested in uncovering the processes involved in DNA repair.

DNA can become damaged by ultraviolet light from the sun, he said, and it is important in terms of preventing cancer that the DNA be repaired as quickly as possible.

“There are very efficient proteins that do this,” Stanley said. “One protein, photolyase, will identify the UV-damaged DNA very specifically and hold on to it and not do anything until it receives a photon of blue or green light. At that point, in about two-billionths of a second, the DNA will be repaired.

“But we know very little about how the damaged DNA is bound by the protein, and we don’t know anything about how the DNA is manipulated,” he said.

Stanley added that the single-molecule microscope would be available for any researchers in other departments, especially “anyone who is interested in how a particular protein functions in real time.”

Recycling waste

Adrienne Cooper, assistant professor of civil and environmental engineering, has received $75,544 from the National Science Foundation’s Small Grants for Exploratory Research Program to examine using waste biomaterials for enzymatic synthesis.

“The idea is, if you have something that is high-risk, high-reward, something new and innovative that hasn’t been tried before, the NSF will provide you with some seed money through SGER basically to do proof-of-concept work,” said Cooper, who joined the College of Engineering faculty from the University of South Carolina in fall 2003.

Cooper is exploring the use of waste as a source of enzymes for the bio-catalytic process for the synthesis of chemical compounds, which in the long term could lead to the development of new or existing materials into more environmentally friendly materials.

“I’m looking at using waste as a resource, one; having it be a bio-catalytic system, two; as well as looking at a number of different solvents with the idea that this bio-catalytic process would be a ‘green’ or environmentally friendly synthesis process,” she said. “We’re trying to identify if there’s a way to do these catalytic processes that makes more sense economically.”

In 2001, Cooper was the recipient of a prestigious five-year NSF CAREER Award, which recognizes and supports the early career-development activities of those teacher-scholars who are most likely to become the academic leaders of the 21st century.

Measuring X-ray polarization

NASA’s Goddard Space Flight Center has awarded $8,000 to physicist C.J. Martoff to begin building a benchtop polarimeter during the next six months. If successful, the prototype — based on a negative ion drift technique developed by Martoff — will allow physicists from the GSFC’s X-Ray Astrophysics Branch to go forward to plan for a space flight payload to do astrophysical measurements.

“X-rays carry a lot of detailed information about the structure and dynamics of astronomical objects, from black holes to our own sun,” Martoff said. “But X-ray astronomy is a very new field because the atmosphere absorbs X-rays from space so strongly that measurements can only be done with instruments in space.”

According to Martoff, most X-ray experiments to date measure only the energy and intensity of X-rays, but much more information can be attained if the X-ray polarization can be measured. Polarization is the property of light that allows polarizing sunglasses to block reflected glare without making the whole scene look dark.

“With X-rays from space, the polarization tells us a lot about how the X-rays are produced, and what the magnetic fields are like in the emitting region,” he said. “This information would help unravel the mysteries of just what happens as matter slips into oblivion at the event horizon of a black hole, or what drives the huge solar flares that disrupt radio communications on Earth.”

Scientists at the GSFC have been working for years to develop a simple and rugged detector that would survive the rigors of space flight, but with very high accuracy to allow the subtle polarization effect to be measured. Detectors based on photoelectric absorption of X-rays in a gas came closest to satisfying these requirements, but there was no method known to make them large enough and at the same time accurate enough to really work well.

Martoff solved this problem when he invented his direction-sensitive dark matter detector called DRIFT, which uses a negative ion drift technique instead of the electron drift that has always been used for gas detectors.

“The ions drift in very straight lines, avoiding the blurring that limits the accuracy of conventional detectors,” Martoff said. “The use of negative ions also greatly stabilizes the gas detector against sparking, which makes it much easier to construct large detectors that will work reliably.”

Preston M. Moretz