A New Take on DNA Sequencing

Scientists have demonstrated a technique that may lead to fast, low-cost reading of whole genomes, through recognition of the nucleotide bases that make up the DNA double helix.

Biophysicist Dr. Stuart Lindsay, of the Biodesign Institute at Arizona State University (Tempe, USA) developed the technique. Dr. Lindsay is director of the Biodesign Institute's Center for Single Molecule Biophysics. His group's research appears in the November 2010 issue of the journal Nature Nanotechnology.

Dr. Lindsay's technique for reading the DNA code relies on quantum tunneling. According to quantum theory, elementary particles such as electrons can do counter-intuitive things, in defiance of classical laws of physics. Such sub-atomic, quantum entities possess both a particle and a wave-like nature. Part of the consequence of this is that an electron has some probability of moving from one side of a barrier to the other, regardless of the height or width of such a barrier.

Remarkably, an electron can accomplish this feat, even when the potential energy of the barrier exceeds the kinetic energy of the particle. Such behavior is known as quantum tunneling, and the flow of electrons is a tunneling current. Tunneling is confined to small distances--so small that a tunnel junction should be able to read one DNA base at a time without interference from flanking bases. However, the same sensitivity to distance means that vibrations of the DNA, or intervening water molecules, destroy the tunneling signal. So the scientist have developed "recognition molecules” that "grab hold” of each base in turn, clutching the base against the electrodes that read out the signal. They call this new method recognition tunneling.

The study shows that single bases inside a DNA chain can indeed be read with tunneling, without interference from neighboring bases. Each base generates a distinct electronic signal, current spikes of a specific size and frequency that serve to identify each base. Surprisingly, the technique even recognizes the epigenetic code.

To read longer lengths of DNA, the researchers are working to couple the tunneling readout to a nanopore--a minuscule hole through which DNA is dragged, one base at a time, by an electric field. "It has always been believed that the problem with passing DNA through a nanopore is that it flies through so quickly that there is no time to read the sequence,” Dr. Lindsay stated.

Amazingly, the tunneling signals last for a long time--nearly a second per base read. To assess this result, Dr. Lindsay teamed with a colleague, Dr. Robert Ros, to measure how hard one has to pull to break the complex of a DNA base plus the recognition molecules. They achieved this with an atomic force microscope. "These measurements confirmed the long lifetime of the complex, and also showed that the reading time could be speeded up at will by the application of a small additional pulling force,” said Dr. Ros. "Thus the stage is set for combining tunneling reads with a device that passes DNA through a nanopore,” added Dr. Lindsay.

Sequencing through recognition tunneling, if shown successful for whole genome reading, could represent a significant savings in cost and hopefully, in time as well. Existing techniques of DNA sequencing typically rely on cutting the full molecule into thousands of component bits, slicing apart the ladder of complementary bases, and reading these fragments. Afterward, the pieces must be reassembled, with the help of massive computing power. "Direct readout of the epigenetic code holds the key to understanding why cells in different tissues are different, despite having the same genome,” Dr. Lindsay noted, referring to the new ability to read epigenetic modifications with tunneling.

Dr. Lindsay stressed much work remains to be done before the application of sequencing by recognition can become a clinical reality.

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Biodesign Institute at Arizona State University