Making DNA Personal

When the Human Genome Project announced it had “cracked the code” of human DNA in 2002, the announcement sparked a worldwide flurry of predictions that the achievement would usher in a new era of personalized medicine. Physicians would be able to diagnose and treat illness more precisely because they could consult the patient’s DNA directly to determine the exact nature of the problem and the medical intervention most likely to treat it.

 

Impressive as it was, the Human Genome Project represented only the first step onto a long, winding road to personalized medicine. For one thing, it took 11 years and millions of dollars to produce a “map” of the human genome, and that was a composite picture of human DNA, not the map of an individual’s code. Faster and cheaper DNA mapping techniques must be developed in order to be of use to an individual patient.

 

For that you need a pretty complex array of devices and techniques that can work at the molecular level, since DNA is a molecule. The problem is that, down at the molecular level, also known as the nanoscale, things get tricky.

 

Deyu Li is studying the dynamics of fluids at the nanoscale level and is harnessing nano eccentricities to zero in on DNA and other important molecules.

 

The assistant professor of mechanical engineering at Vanderbilt has developed a sensing technique that can be up to two orders of magnitude more sensitive than current, similar techniques. The device will be able to signal when a single molecule has entered the sensing channel and, he hopes, will ultimately be able to “read” the DNA molecule as it passes through the channel.

 

 “Sensors have been developed that can sense single DNA molecules,” Li says. “Currently these devices still need to improve their sensitivity and dynamic range. Our device significantly strengthens the sensitivity of the sensor.”

 

 His device does that by incorporating a workhorse device borrowed from computer technology, a transistor called a MOSFET (for metal-oxide-semiconductor field-effect transistor). The MOSFET effectively amplifies the signal from the sensing channel. This amplification makes it possible to detect small signals from the sensing channel, which with the existing technique cannot be distinguished from “noise.” He hopes that, ultimately, the new technique can help to sense the subtle electrical signals that individual DNA bases (DNA building blocks) produce so they can be identified.

 

 “By amplifying the electrical signals emanating from our sensing channel, we are heightening the precision of existing nanofluidics sensing technology.”

 

Nanofluidics

 

Nanofluidics is the field devoted to fluid behavior in confined nano-environments. At bulk quantities of fluids, the interactions of molecules in the fluid with a container or channel are negligible. Those interactions become more crucial as the molecules flow through channels or pores several nanometers wide (a nanometer is equivalent to one billionth of a meter). For example, simply changing the electrical charge of a container can have a dramatic effect at the nano level.

 

“Nanoscale phenomena present both obstacles and opportunities,” Li says. “On the one hand, nano size is a challenge because minute variations of the surfaces of the channels and pores can cause clogs. But that same sensitivity becomes an advantage in controlling nanoscale flow, because molecules tightly contained in nanochannels are so sensitive to the electrical characteristics of their containers. We can alter the electrical charge on the channel wall in such a way that it propels the liquid in a desirable direction.”

 

 This technique allows engineers to tightly calibrate the fluid flows at the molecular level through the control of electroosmotic flow, which is produced by applying a voltage to the ends of the channels. The voltage will cause a net flow of the liquid inside the channel, and molecules suspended in the electrolyte are swept along with the current.

 

To determine that a molecule is passing through the sensing chamber, Li adapted a technique called Coulter counting. “Coulter counting senses changes in electrical conductance of a channel as a particle or cell passes through it.”

 

 Since the changes in electrical conductance are so minute for single molecules, it is difficult to get a precise measurement. Li decided to use aMOSFET to amplify the changes.

 

 “MOSFETs are designed to conduct current when the electrical potential on their gate is intensified,” Li said. “The amount of current can be varied by varying the gate potential.”

 

By combining the Coulter counting principle with the MOSFET’s amplification of signal, Li’s device has achieved a minimum volume ratio of the particle to the sensing channel of only 0.006 percent, which is about ten times smaller than the lowest reported detectable volume ratio. That means that much smaller particles can be detected than before. “Theoretical analysis showed that the technique can be 100 times more sensitive,” Li said.

 

The device proved itself at the micro level, as published in Applied Physics Letters. Li and his collaborators tested the device using microbeads of polystyrene. “Amplification is achieved by both the fluid circuit and the MOSFET. We believe the sensing mechanism will be applicable to nanochannels for single-molecule detection.”

 

When the device is scaled to the molecular level, it can be used not only in DNA analysis but can play an important role in the development of new drugs and the detection of disease. It is already being used at Vanderbilt to count white blood cells for portable HIV diagnostic devices.

 

Li’s work has won him recognition and funding from National Science Foundation, which awarded him a 2007 CAREER award for his research into nanofluidics. Acknowledging that much remains to be accomplished to adapt his device to the nanoscale, he is hopeful that soon his device will help bring the dream of personalized medicine several steps closer to being realized.