Carnegie Mellon University
March 20, 2007

Fluorescence Guru: Alan Waggoner Illuminates a Field

By Amy Pavlak

Intense sunlight beats down on chemist Alan Waggoner as he examines a fossil in Chile's Atacama Desert. From his mountain perch, Waggoner has an excellent view of Zoë, Carnegie Mellon's autonomous rover. While Waggoner scans the fossil he's holding for vestiges of life, Zoë has a much larger task - canvassing kilometers of desert terrain for faint signs of life existing in this inhospitable landscape.

Zoë is no ordinary robot. She's equipped with a fluorescent imaging system tricked out with a set of four dyes developed by Waggoner and his colleagues at the Molecular Biosensor and Imaging Center (MBIC). The dyes bind to the basic components of life - DNA, lipids, carbohydrates and proteins - and emit a fluorescent glow that Zoë captures on its onboard camera.

As Zoë treks across the desert, spraying dyes as she goes, Waggoner can't resist the diversion of inspecting the area's fossils. For him, science - and life - is a balance between serendipitous encounters with nature and focusing his mental lens on scientific problems that look initially as insurmountable as the course Zoë is attempting to execute.

Waggoner, professor of biological sciences at the Mellon College of Science and director of MBIC, doesn't limit himself to investigating what he can see with the naked eye. Since the 1980s, his laboratory has developed and refined a set of fluorescent dyes that have allowed scientists around the world to delve into the mysteries hidden inside cells.

"Alan is one of the top scientists developing fluorescent probes," says C. Jeffrey Wang, Alan's first postdoc at Amherst College who is now president of Spherotech, a company that manufactures uniform fluorescent and various colored microparticles for biomedical and diagnostic applications. "Alan's fluorescent dyes are some of the most commonly used in biomedical research."

Waggoner's cyanine dyes, CyDyesTM, have played a significant role in analyzing how genes switch on and off to regulate cells and tissues. The fluorescent dyes aboard Zoë's fluorescent imager are iterations of the CyDyes. Now, MBIC scientists are creating new versions to image heartbeats and witness the dynamic world of protein interactions within and between living cells.

Synergy Across Disciplines

Today, fluorescence-detection is a multi-billion-dollar industry that provides the foundation of many different technologies used in basic biological studies, as well as disease diagnosis and treatment. Waggoner's career and dye technology evolved in unison. In the 1970s, when Waggoner was starting his career, fluorescence was in its infancy. Available dyes had problems. They chemically stuck to everything, including each other, which hampered their ability to fluoresce. Some dyes were easy to work with chemically but didn't give a good fluorescent signal. Worse still, many dyes were toxic to cells.

Such obstacles discouraged many of his contemporaries, but Waggoner tackled the challenge with zeal. While he was at Amherst College in the mid-1970s, he teamed up with physiologist Larry Cohen, who was interested in studying communication between neurons. In his quest to design a stable, non-toxic dye that would do the trick, Waggoner synthesized thousands of versions until he created one that became the first that could easily sense electrical activity in neurons. His voltage-sensitive dye was lauded in the science world - and it put Waggoner's name on the map.

"He quickly became a legend," says Greg Fisher, senior research scientist at MBIC. "Alan really pushed the development of fluorescent labels to design practical dyes for sensing what was going on in living cells."

While at Amherst, Waggoner was recruited by Lans Taylor, then professor of biological sciences at Carnegie Mellon. Taylor was interested in creating a center at Carnegie Mellon that would couple fluorescent probes with imaging systems and apply them to questions in cell biology. Waggoner's expertise in dye development was key to the new center's success. Recognizing a great opportunity, Waggoner joined Taylor at Carnegie Mellon's Center for Fluorescence Research, which was renamed the Center for Light Microscope Imaging and Biotechnology in 1991 and today goes by MBIC.

Inspiration From Art

When Waggoner arrived at Carnegie Mellon in 1982, biologists were limited by the fluorescent probes and labels for protein and DNA available at that time. They needed more dyes in an assortment of colors to really understand what was going on with living and fixed cells.

"Alan is an excellent chemist, and he loves being a chemist. But his real strength is his ability to talk with biologists, identify areas where new chemical tools are needed to tackle significant biological problems, and then create teams who can build those tools," explains Kathy Muirhead, chief operating officer of SciGro Inc., who has taught with Waggoner for more than 25 years at training courses for scientists interested in studying cell functions and interactions using fluorescent probes and flow cytometers. "He's a scientific popcorn machine. He has an idea a minute, and no idea is too crazy to consider. That's what makes him so much fun to work with!"

An amateur photographer, Waggoner drew his inspiration from the cyanine family of dyes that were used at the time to produce a variety of colors on photographic film. Although colorblind and unable to distinguish red from green, Waggoner didn't let his sight get in the way of his vision. He systematically engineered properties within each cyanine dye molecule to make them photostable, water soluble and minimally toxic. And they had the appropriate reactivity and efficiency of emission.

"Alan has a vision and a practical sense of what can be done. He really enhanced the fluorescent properties of the CyDyes, engineering them to have the properties needed to make them successful for use in living cells," Fisher says.

"Two of the cyanine dyes - Cy3 and Cy5 - are thebenchmarks in stable dyes," explains MBIC Senior Research Scientist Lauren Ernst. "These dyes laid the groundwork for the competition."

Waggoner patented the CyDyes, the first of his 27 patents, and spun out Biological Detection Systems Inc. (BDS) with Taylor to commercialize the dyes and instruments to detect them. Waggoner served as vice chairman of BDS, and when BDS technologies were acquired by Amersham PLC, he joined that company as principal scientist and head of fluorescence. Amersham, now GE Healthcare, still holds the active license to the dyes and their related products, which remain the intellectual property of Carnegie Mellon. In May 1999, when Amersham consolidated its acquisitions in New Jersey, Waggoner returned to Carnegie Mellon as director of what is now MBIC. Under Waggoner's leadership, MBIC has become world renowned for its expertise in biochemistry, genetics, dye chemistry and imaging.

Over the years, Waggoner and his team have synthesized thousands of dyes, and they've never thrown any of them away. This pack-rat mentality is paying off. MBIC scientists are chemically tinkering with the leftover dyes and have found that, under the right conditions, the dyes can change their fluorescence properties. With a little imagination and ingenuity, the possibilities for their uses are virtually endless.

Although Zoë has finished her journey, Waggoner is taking the life detection technology on the road - perhaps in the form of a public health biomedical backpack. And Waggoner couldn't be happier.

"This is a great adventure. There is a nice family here, and together we can do some pretty amazing things."