It's a Small World
by Will SansomTo view large but immensely distant single stars, The University of Texas operates the McDonald Observatory in West Texas. In comparable fashion, biochemists at the Health Science Center use the latest light microscopes and high-sensitivity video cameras to view single biological particles that are close, but very small.
Pretend you are on an airplane at 30,000 feet above sea level, it’s a dark, moonless night, and you want to look through the plane’s window to see one hummingbird at the feeder in your back yard. Your only equipment is a flashlight on the seat beside you. Can you see the bird? Yes, if the flashlight is powerful enough to reach the feeder area and if the bird returns the light with a color that distinguishes it from its surroundings. All things considered, you still won’t be able to see the bird’s exact form or pinpoint its precise location in the back yard.
This example illustrates the challenge facing Philip Serwer, Ph.D., and Rui J. Sousa, Ph.D., professors of biochemistry in the Health Science Center’s Graduate School of Biomedical Sciences. Their research teams are capturing details of the molecular behavior of biological particles while looking through the window of optical instruments. They are examining objects a billion times smaller than a meter. (One billionth of a meter is called a "nanometer" because billion has nine zeroes. "Nano" is derived from the Greek word for nine.) This is nanoscience and nanotechnology – science and technology at the scale of the nanometer ndash; and resembles the task of spying on a hummingbird at night from an airplane window with a flashlight.
"Our long-range goal is to study the complex reactions that take place during a single biochemical event," Dr. Serwer said. "We know that bacterial viruses (called bacteriophages) are assembled by packaging a DNA molecule in a protein outer shell. We are observing this activity as it happens and are recording it for study, one packaging event at a time."
Dr. Serwer’s team labels the protein shells with a fluorescent dye and the DNA molecules with a dye of a different color. These dyes make single particles visible during fluorescence microscopy. "In our hummingbird example, if we color the hummingbird green and the feeder red, we can use the color difference to distinguish the two," he said.
The microscope bathes the particles with bright light and filters out background light. The particles emit their own light signatures. "Under the microscope, the protein shells resemble stars moving across the night sky," Dr. Serwer said. "DNA molecules are sometimes stretched so that they resemble a molecular noodle."
The scientists compute a particle’s size by studying its thermal motion (random movements that increase in speed as temperature rises). Viral particles generally are between 20 and 160 nanometers in diameter. "The challenge is to make sufficient measurements of a collection of the active particles so that the biochemical events can be analyzed," Dr. Serwer said. By using a high-sensitivity video camera and advanced color-recording procedures during fluorescence microscopy, his group has made movies of DNA packaging in real time.
Indeed, the frontier of modern biochemistry is to step beyond still pictures of molecules to dynamic movies of them. Molecules act like machines or robots with moving parts. Understanding interactions between molecules, such as the way they bind to each other, could lead to effective new disease therapies.
Dr. Rui Sousa’s team is utilizing new techniques to make a movie of one of the most basic biological molecules, RNA polymerase. "RNA polymerase copies DNA into RNA, which is then translated into proteins that carry out all of the reactions in the body," he said. "It works like a microscopic machine that strings together letters (nucleotides) following the instructions of the DNA template. By studying RNA polymerase, we may learn how to make our own purpose-specific ‘nano-machines,’ which would be so small that a billion of them could be suspended in one milliliter of water and injected into a person’s bloodstream where they could, for example, bust up a blood clot, destroy a tumor or fix a defective gene."
This potential has not been realized, but already Dr. Sousa’s lab has engineered RNA polymerase to make it more useful for therapeutic applications. "A lot of people want to use RNA for therapeutic purposes, but one problem is that natural RNA is rapidly digested in our bodies," he explained. "If the RNA is made with specially modified nucleotides, however, it becomes resistant to digestion, persists longer in the body and is a more effective drug.
"The problem is that natural RNA polymerase doesn’t like to make this modified RNA. What we did is engineer the RNA polymerase so that it will make this special, digestion-resistant RNA. A lot of labs now are using this patented, engineered RNA polymerase. A Norwegian group, for example, found it is possible to block brain tumor growth in mice with a therapeutic RNA, but only by using a digestion-resistant version of the RNA made with our engineered RNA polymerase." Dr. Serwer sees the biochemists’ work as "opening a way for ourselves and other scientists to study the activities of single ‘nano-particles.’ Other research groups around the country – Harvard, Stanford, the University of Minnesota and the University of California, San Diego – are some of those doing similar work." This is the work of seeing and making observations about a proverbial hummingbird – be it a single viral particle or a single molecule – from an equally proverbial airplane window.
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