BioMEMS Laboratory Research

Borrowing the best from biology, physics, and precision engineering, the Whitehead BioMEMS lab is developing a new generation of tools that is reshaping how biology is done. These new tools, including an ultrafast DNA sequencing device are tackling complex biological problems and bringing into sharp focus many of life’s intricacies.

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Generating Genome Sequences

From expanding the frontiers of pharmaceutical research to charting life’s evolutionary origins, DNA sequencing has emerged as one of the most exciting

research tools of the twenty-first century. Improving this already invaluable tool, the BioMEMS lab has developed a way to make DNA sequencing faster, more accurate, and exponentially less expensive than ever before. The centerpiece of this effort is a chip-based DNA sequencing device that miniaturizes a process called electrophoresis—a method commonly used to sequence DNA—onto a small glass chip. Developed from the ground up at Whitehead, the sequencer is

the collaborative work of biologists, engineers, chemists, and physicists. The device sequences a fragment of DNA as the DNA is passed through microchannels etched onto the surface of a glass chip. When a sample is injected into the chip’s channels, an electric current separates the DNA molecules based on their size.

By reducing the cost and miniaturizing the process, the chip-based sequencer will make DNA sequencing accessible to smaller labs, says Paul Matsudaira. “Instead of needing a full-scale genome center to perform high-throughput sequencing, researchers with a few cubic feet of lab space will have the ability to rapidly and accurately sequence DNA.” The switch to chip-based sequencers reduces both the amount of lab space needed and the amount of reagents and enzymes that make DNA sequencing a costly endeavor. The device is fully automated, reducing labor costs and ensuring more reliable results.

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Science for life: Celebrating 20 years of discovery

Faster Fingerprinting

Improvements in chip technology are so promising that the BioMEMS lab has prepared a similar version of the chip for use in DNA forensics. Many criminal cases across the country are stuck in legal limbo because authorities have to wait weeks, sometimes even months, for DNA test results. Scientists use the chip-based sequencers to identify DNA landmarks called “STRs,” or short tandem repeats, from samples collected at a crime scene. Much like a fingerprint, these STR landmarks are unique to an individual and can be used to identify a person by his or her DNA. Unlike existing DNA sequencers this instrument is portable and can be part of a mobile crime lab, providing crime scene investigators with the ability to turn evidence into information on the spot, dramatically improving the value of DNA evidence in solving crimes.