Dancing DNA: tripping the light fantastic with heredity's master molecules - using fluorescence microscopy to image the DNA molecule

Science News, August 3, 1991 by Elizabeth Pennisi

His work will never win an Emmy, but Japanese biophysicist Mitsuhiro Yanagida nevertheless made television history a decade ago when he captured DNA in a crude black-and-white action video. Borrowing the concepts and camera technology used by astronomers, the Kyoto University scientist became the first to film individual DNA molecules - live. The footage attracted little attention at the time, and Yanagida eventually moved on to other work.

Now several U.S. scientists have adopted his approach to witness the dance of individual DNA molecules as they twirl and snake through gels or bend and stretch in solution. The researchers' success in solving a long-standing mystery about how gels can sort DNA molecules by size convinces them that this imaging technique - which uses fluorescence microscopy - will revolutionize molecular biology and materials science.

"We're developing single-molecule methodologies for doing molecular biology," says David C. Schwartz, a biophysicist at New York University in New York City. "The field is going to break wide open."

Through the eyepiece of his microscope, and then at his computer screen, Schwartz plans to pinpoint genes on chromosomes and study the interactions between DNA and certain proteins. Carlos Bustamante and Steven B. Smith at the University of Oregon in Eugene use a similar system to investigate how DNA and chromatin - chromosomal DNA tightly bound to histone and other proteins - fold into their functional forms. The Oregon researchers are now testing the mechanical properties of these molecules, and they anticipate they day when they can manipulate the molecules as well as watch them.

Chemists have begun eyeing the technique as a means to improve their understanding of the dynamics of polymers and other long, complex molecules. Even the Department of Defense expresses interest: Bustamante may get some stunning footage of polymers quelling turbulence later this year, which could help Navy scientists develop techniques for reducing friction on its vessels.

"The idea that you can see the molecules and how they behave is very important," says Bustamante.

While certainly of scientific interest, the images may also offer technological insights. Studies of protein folding and of DNA movements could speed the development of useful protein-based products and of new purification procedures for biotechnology, Bustamante suspects. Research into polymer dynamics may lead to more versatile plastics, or perhaps to new polymer lubricants.

The imaging technique defies the conventional wisdom that optical microscopes cannot resolve something as tiny as a molecule. "We play a trick," Bustamante admits. The secret lies in the design of the experiment and in the length of the DNA.

The technique involves attaching a fluorescent dye to DNA molecules to form a complex that glows. "What you actually see is the dye," explains Yuqiu Jiang, a graduate student working with Bustamante. Light shining down through the microscope cause the dye in the sample to fluoresce, and a filter blocks any stray light that might otherwise reflect back through the eyepiece.

Thus, just as one can watch very distant stars inch across a dark sky, these researchers can track the glowing DNA as it moves against a dark background. Indeed, the molecules look a little like shooting stars: Their leading ends shine brighter than their trailing tails. The researchers cannot resolve the molecule itself in much detail, but they can follow its movements.

"That's the beauty of it," Schwartz says. "You can watch the molecules and see what is going on."

"We can basically do chemistry with a single DNA molecule," Bustamante says. He has built a tiny experimental chamber for this work. He puts a molecule inside and magnifies it - first through the microscope's optics, then many times more as he blows up the image on a TV monitor. The squiggle that swims across the screen appears more than 5,000 times its original size.

Getting a good image, however, has proved quite challenging, Bustamante reports in the 1991 Annual Review of Biophysics and Biophysical Chemistry. Through experimentation, he learned how much dye to use. Too little dye resulted in a faint image, but too much dye in the sample created light pollution, making the DNA specks difficult to follow. Over time, he added an image intensifier that helps make weak picture signals clearer. He and his colleagues have also gleaned the importance of making sure their apparatus is properly grounded so that motors, lamps and other fixtures do not create spurious background signals.

Schwartz' team at NYU linked the camera that records their microscopic subjects directly to a computer, which digitized and enhances the image.

Both groups initially used their microscope-video systems to study DNA's movement through electrophoretic gels. A standard technique for separating DNA pieces of different sizes, electrophoresis relies on an electric field to gently draw charged DNA particles of varying sizes down a gel. Though molecular biologists depend on gels for electrophoresis, they never really understood how the technique worked.