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GEN News Highlights : Feb 12, 2010

Nanotech-Based DNA Sequencer that Distinguishes between the Four Bases Developed

Tweaking the reader to work in water-based solutions and with carbon nanotube technology is the next step, as reported in Nano Letters.

Arizona State University scientists report having developed a reader that can discriminate between DNA's four chemical components. Details appear in Nano Letters in a paper titled “Electronic Signatures of all Four DNA Nucleosides in a Tunneling Gap.” ASU Regents' professor Stuart Lindsay, Ph.D., led the research.

In 2008, Dr. Lindsay's team demonstrated the ability to read individual DNA sequences, but this approach was limited because they had to use four separate readers to recognize each of the DNA bases. More recently, they demonstrated the ability to thread DNA sequences through a carbon nanotube. The group used scanning tunneling and atomic force microscopes to make their measurements. The microscopes have an electrode tip that is held very close to the DNA sample.

In their latest innovation, Dr. Lindsay's group made two electrodes, one on the end of a microscope probe and another on the surface. The end of each was chemically modified to attract and catch the DNA between a gap like a pair of chemical tweezers. The gap between these functionalized electrodes had to be adjusted to find the chemical bonding sweet spot so that when a single chemical base of DNA passed through a 2.5-nanometer gap between two gold electrodes, it momentarily sticks to the electrodes and a small increase in the current is detected. Any smaller and the molecules would be able to bind in many configurations, confusing the readout. Any bigger and smaller bases would not be detected.

“What we did was to narrow the number of types of bound configurations to just one per DNA base,” Dr. Lindsay explains. “The beauty of the approach is that all the four bases just fit the 2.5 nanometer gap, so it is one size fits all but only just so!”

At this scale, which is just a few atomic diameters wide, quantum phenomena are at play where the electrons can actually leak from one electrode to the other, tunneling through the DNA bases in the process. Each of the chemical bases of the DNA genetic code gives a unique electrical signature as they pass between the gap in the electrodes. By trial and error and a bit of serendipity, the researchers admit, they discovered that just a single chemical modification to both electrodes could distinguish between all four DNA bases.

“We've now made a generic DNA sequence reader and are the first group to report the detection of all four DNA bases in one tunnel gap,” according to Dr. Lindsay. “Also, the control experiments show that there is a certain (poor) level of discrimination with even bare electrodes (the control experiments) and this is in itself a first, too.

“We were quite surprised about binding to bare electrodes because, like many physicists, we had always assumed that the bases would just tumble through. But actually, any surface chemist will tell you that the bases have weak chemical interactions with metal surfaces.”

Next, Lindsay's group is hard at work trying to adapt the reader to work in water-based solutions, a critically practical step for DNA sequencing applications. Also, the team would like to combine the reader capabilities with the carbon nanotube technology to work on reading short stretches of DNA.