A new read on DNA sequencing

November 17, 2010

The twisting, ladder-like form of the DNA molecule – the architectural floor plan of life – contains a universe of information critical to human health. Enormous effort has been invested in deciphering the genetic code, including, most famously, the Human Genome Project. Nevertheless, the process of reading some 3 billion nucleotide "letters" to reveal an individual's full genome remains a costly and complex undertaking.

Now, Stuart Lindsay, biophysicist in ASU’s Biodesign Institute, has demonstrated a technique that may lead to rapid, low-cost reading of whole genomes, through recognition of the basic chemical units – the nucleotide bases that make up the DNA double helix. An affordable technique for DNA sequencing would be a tremendous advance for medicine, allowing routine clinical genomic screening for diagnostic purposes; the design of a new generation of custom-fit pharmaceuticals; and even genomic tinkering to enhance cellular resistance to viral or bacterial infection. Download Full Image

Lindsay is an ASU Regents' Professor and Carson Presidential Chair of Physics and Chemistry, as well as director of the Biodesign Institute's Center for Single Molecule Biophysics. His group's research appears in the current issue of the journal Nature Nanotechnology.

Lindsay's technique for reading the DNA code relies on a fundamental property of matter known as quantum tunneling, which operates at the subatomic scale. According to quantum theory, elementary particles like electrons can do some very strange and counterintuitive 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 (there are four of them in the gentic code, A,T,C and G) at a time without interference from flanking bases. But the same sensitivity to distance means that vibrations of the DNA, or intervening water molecules, ruin the tunneling signal. So the Lindsay group has 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 current paper in Nature Nanotechnology 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 particular size and frequency that serve to identify each base. Surprisingly, the technique even recognizes a small chemical change that nature sometimes uses to fine-tune the expression of genes, the so-called "epigenetic" code. While an individual's genetic code is the same in every cell, the epigenetic code is tissue and cell specific and unlike the genome itself, the epigenome can respond to environmental changes during an individual's life.

To read longer lengths of DNA, Lindsay's group is working to couple the tunneling readout to a nanopore – a tiny hole through which DNA is dragged, one base at a time, by an electric field. The paper in Nature Nanotechnology has something to say about this problem too.

"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," Lindsay said. Surprisingly, the tunneling signals reported in the paper last for a long time – nearly a second per base read.

To test this result, Lindsay teamed with a colleague, Robert Ros, to measure how hard one has to pull to break the complex of a DNA base plus the recognition molecules. They did 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," Ros said.

"Thus the stage is set for combining tunneling reads with a device that passes DNA through a nanopore," Lindsay said.

Sequencing through recognition tunneling, if proven successful for whole genome reading, could represent a substantial savings in cost and hopefully, in time as well. Existing methods of DNA sequencing typically rely on cutting the full molecule into thousands of component bits, snipping apart the ladder of complementary bases and reading these fragments. Later, the pieces must be meticulously re-assembled, with the aid 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," Lindsay added, a reference to the new ability to read epigenetic modifications with tunneling.

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

"Right now, we can only read two or three bases as the tunneling probe drifts over them, and some bases are more accurately identified than others," he said. However, the group expects this to improve as future generations of recognition molecules are synthesized.

"The basic physics is now demonstrated" Lindsay said, adding "perhaps it will soon be possible to incorporate these principles into mass produced computer chips."

The day of the "genome on a lap-top" might be coming sooner than previously thought possible.

Britt Lewis

Communications Specialist, ASU Library

Alum's medical success born of ASU experience, community service

November 17, 2010

A passion for family medicine, kindled by undergraduate studies in the School of Life Sciences and service as a Spanish translator, created a journey toward success for ASU alumna Sarah Louie Lusk. Lusk recently received the David E. Rogers Award for Community Service along with her medical degree from Johns Hopkins School of Medicine and was accepted into a medical residency with University of California, Los Angeles (UCLA) Department of Family Medicine – thanks in large part to early mentorship at ASU.

Lusk’s journey from Tempe, Ariz. to Baltimore, Md., to Los Angeles started when she was a 2006 Barrett Honors College undergraduate majoring in biology with a concentration in biology and society. In addition to her coursework, Lusk volunteered as a Spanish interpreter in the Centro de Salud Health Clinic, which serves uninsured Latino patients in Phoenix, Ariz. There, Lusk became interested in how the language used by health care providers, English or Spanish, impacts the experience and health care decision-making of the clinic's Spanish-speaking patients. She became so interested in this question that she decided to develop her Honors Thesis "Health promotion and disease prevention in Nuestro Barrio" around extensive interviews of patients at the clinic, with support from her advisor Jane Maienschein, a Regents’, President’s and Parents Association Professor in the School of Life Sciences in the College of Liberal Arts and Sciences.
Lusk’s work with Maienschein led to the award of a travel grant through the Barrett Honors College and the Center for Biology and Society. Such support allowed Lusk and other honors college and School of Life Sciences’ undergraduates to go to the American Association for the Advancement of Science (AAAS) annual meeting in St. Louis, Missouri, in 2006. This experience, Lusk says, helped her appreciate scientific conferences and how scientific information is communicated in a public setting. Download Full Image

"I presented the findings of my interviews at Centro de Salud and it was an amazing opportunity, not only to share my work, but also to see what other students and researchers with similar interests were investigating," Lusk said. "Dr. Maienschein really allowed me to pursue my passion and gave me the tools to present what I had learned on a national stage. It taught me the value of dialogue in the scientific, ethics and now medical community of which I am a part."

While interested in medicine since elementary school, Lusk's early experience in the clinic between her sophomore and junior undergraduate years and mentorship in her studies solidified her desire to learn and practice family medicine in an underserved community. As her medical training unfolded at Johns Hopkins School of Medicine, she continued to work as an interpreter in the school's Latino clinic in East Baltimore. In addition, she also served as a mentor for local area high school students.

While her recognition as a David E. Rogers Award winner – given to two graduating seniors in each Hopkins medical class for professionalism, medical ethics and community leadership – was a surprise to Lusk, it came as no surprise to those at ASU familiar with her experiences as an undergraduate.
Maienschein, who is also the director of the Center for Biology and Society in ASU's School of Life Sciences, remembers Lusk's interest in bioethics while at ASU. "She was a leader and part of the group that established the Bioethics Club, which in turn led to the development of other programs at the center. These included the Bioethics Films Series and the Western Regional Bioethics Conference,” Maienschein said. “The conference was wildly popular and brought students from all over the West to ASU. In fact all six of the organizers have gone on to be community leaders, like Sarah."

“I couldn't have been more proud,” said Pam Lusk, Sarah’s mother. “I can't think of a more meaningful recognition than for medical ethics, professionalism and leadership in the community. Sarah certainly was a stand out in a very, very talented class of medical students. Also a very fitting award for an ASU biology and society major, don't you think?”
This fall, Lusk started her medical residency in the department of family medicine at UCLA, where she has begun working in the county clinic. After her residency, she hopes to continue to provide medical care for underserved patient populations and help develop a community model where each community defines its own medical needs.

“I had an amazing time at ASU and am thankful for its role in finding and helping me develop my passion for family medicine,” Lusk said. Undoubtedly, this award-winning physician, one of the many successful alumni from the School of Life Sciences, has a great future ahead, built on access to an excellent foundation, both in experience and individualized support.

Written by Dan Garry

Margaret Coulombe

Director, Executive Communications, Office of the University Provost