Aksimentiev finds his place with DNA Sequencing Challenge

Sequencing DNA through a synthetic nanopore is the goal of a team of Beckman Institute researchers who were awarded $2.1 million for the project by the National Human Genome Research Institute.

The opportunity is great but so are the expectations. A lot is riding on the outcome of DNA sequencing research and technology development, including researchers hope, results that will some day allow the early diagnosis and treatment of diseases that have resisted medical efforts until now.

Last year the National Human Genome Research Institute (NHGRI) announced a $32 million grant program aimed at accelerating research for a breakthrough gene sequencing technology that is accessible, fast, and inexpensive. The name of the grant program — Revolutionary Genome Sequencing Technologies — portends both its purpose and its desired effect on medical research. The hope is to dramatically change everything from treatment to cost to the gathering of scientific knowledge through low-cost, efficient DNA sequencing. By revealing the information found in DNA (deoxyribonucleic acid), a chemical compound containing the genetic instructions all organisms need for development and direction of their activities, the genetic basis for pathologies such as cancer or heart disease could be found.

A team of researchers at the Beckman Institute for Advanced Science and Technology was one of the groups awarded grant money, receiving $2.1 million for sequencing a DNA molecule using a synthetic nanopore. The group includes top scientists from the fields of computational electronics (Jean-Pierre Leburton and Gregory Timp), theoretical biophysics (Klaus Schulten) and chemistry (Steven Sligar).

There is one more member of the team who is not yet as well known, but who has already contributed one of the group's first big breakthroughs. Using software from Schulten's Theoretical and Computational Biophysics group, researcher Aleksei Aksimentiev was able to do the first-ever simulation of DNA translocation through a synthetic nanopore.

It was an important first step in the team's goal of creating what has been referred to as a low-cost, reliable “gene chip” for sequencing DNA. The technology would use a type of silicon integrated circuit that incorporates a nanopore mechanism through which DNA molecules are forced. The narrow nanoscale opening changes the structure of single strand DNA, causing its base to tilt and the molecules to oscillate back and forth, thereby producing a unique electrical signal. These signals can then be read for the information contained in the individual DNA.

Each member of the team has a specific role in bringing a gene chip to reality. But for Aksimentiev, who knew little of biophysics three years ago, membership on the team is more than a role. It is the realization of an unexpected opportunity.

Aksimentiev grew up in the Ukraine with parents who are scientists — his mother is a chemistry professor and his father a physicist. He earned a cum laude Ph.D. in chemistry from the Institute of Physical Chemistry in Warsaw, Poland.

DNA research wasn't part of Aksimentiev's curriculum vitae when he came to Illinois in 2001. But he saw an opportunity with Schulten's group — known worldwide for molecular dynamics simulations — and was not afraid to follow his instincts. He wrote to Schulten while working for a private company in Japan because, he said, “I was in particle physics and polymer theory and I just wanted to do theoretical biophysics. And the theoretical biophysics group of Klaus' is probably the best.”

After joining TCBG, Aksimentiev worked on ATP synthase, a large multi-protein complex. It was during that time that he heard about the gene chip project.

“To me it looked like a fantastic thing,” said Aksimentiev, an Assistant Professor of Physics at the University of Illinois. “It was a project that didn't have enough people computation-wise. It looked very, very attractive to me.”

Aksimentiev joined the project enthusiastically.

“I thought it was a fantastic idea of bringing silicon and biomolecules into one thing, and nanopores is just one example of that,” he said. “Plus it's very important, because if it succeeds it will be something that is very useful.”

How useful may not be known for 10 or 20 years, but the potential applications of gene research are revolutionary. The NHGRI is the government agency behind the Human Genome Project, which sequenced and mapped the human genome (the aggregate of the genes of Homo sapiens) in 2003, allowing scientists to read the complete genetic blueprint for a human being.

Researchers at NHGRI and the National Institutes of Health, writing about completion of the Human Genome Project, said that “genome sequences, the bounded sets of information that guide biological development and function, lie at the heart” of a revolution in understanding organisms at the molecular level. “In short,” they wrote in Nature in 2004, “genomics has become a central and cohesive discipline of biomedical research.”

Genomics have also been an expensive undertaking. The NHGRI estimates that DNA sequencing costs have fallen by more than 50 fold in the last 10 years, but that it still costs around $10 million to “sequence 3 billion base pairs — the amount of DNA found in the genomes of humans and other mammals.

The oft-repeated goal is to do sequencing for less than a thousand dollars. That's where the gene chip could prove especially useful. Aksimentiev said the process proposed by his group involves forcing single DNA strands through an opening one nanometer wide in an artificial metal-oxide-semiconductor membrane.

“When you put DNA in a very narrow place it behaves differently than when it's in a solution,” Aksimentiev said. “What we discovered was that when we confine a single DNA strand to a very narrow pore, the DNA bases tilt. If you move the strand back and forth in the pore, the tilt of the bases will change its direction and that is what we think will be the signal for us to detect.”

Aksimentiev compared the process to retrieving the signals from a recording.

“The way you would use a magnetic head in a tape recorder, you thread a tape through and you're trying to read a signature,” he said. “In the case of a tape recorder it's a magnetic signal but in the case of DNA we're basically reading different electrical potentials that are written along the strand.”

In a 2005 paper in Bell Labs Technical Journal titled “Beyond the Gene Chip,” Aksimentiev, Schulten, Timp, and others wrote that “molecular dynamics provides us with a means to design (the gene chip) and analyze the experimental outcomes.”

Modeling the operation of the gene chip with molecular dynamics is Aksimentiev's role in the project. He is developing a numerical model of the nanopore sensor to test its design and detection capabilities. These simulations will give the team an understanding of the dynamics of the translocation process that is essential to successful development of a gene chip.

“What we saw was we could take a look at DNA, how it goes through (the nanopore),” Aksimentiev said of the simulations. “We noticed that it is a very, very complex process. DNA is not a rigid rod as people very often picture it. It has all kinds of conformational dynamics that are interesting.

“So what we discovered basically was the time scale for the translocation, how fast it could go, and we saw that indeed it goes very, very fast. We couldn't really measure that before because the resolution of the measurement was not good enough. With simulation you can see that it actually goes very fast.”

Aksimentiev said simulations tell researchers about the electrical signals resulting from the DNA-nanopore interaction and will tell them how to read the signal. The fact the nanopore is solidstate makes the system robust and able to perform in ways other detectors can't.

The grant received by the Beckman group and other researchers will aid biomedicine in ways other than reducing cost, according to NHGRI Director Francis S. Collins.

“Not only will these technologies substantially reduce the cost of sequencing a genome, but they will provide a quantum leap in the scope and scale of research aimed at uncovering the genomic contributions to common diseases, such as cancer, heart disease and diabetes,” Collins said.

That's a tall order, but Aksimentiev says the unique combination of interdisciplinary collaborations and facilities found at Beckman provide the support needed for success.

“One person who really pushed me doing this was Greg Timp,” he said. “He was a fantastic collaborator. I started this project and very quickly I got some results and since then, he wants more and it's great. We are on the same floor and we meet maybe every other day, so it's a continuous flow of information back and forth.

“The other thing that is very important is the TCB group has actually developed software I can use.”

Aksimentiev was referring to the NAMD coding software the TCB group uses to do atomic-scale simulations of biomolecular systems. Aksimentiev used NAMD to complete the first simulation of DNA translocation through a synthetic nanopore.

“I don't think this would be possible anywhere else,” Aksimentiev said of working with the TCB group on the simulation. “I could just stop by next door. That's just something you can't replace or find anywhere else.

“The fact that I was in that group when I started is also very important because I had the expertise of all of them, so I could make a jump to the next level and simulate silicon.”

Aksimentiev said he has also benefited from working with Leburton, an expert in computational electronics.

“He is over the entire device simulation, a higher scale than what we do,” Aksimentiev said. “It has also been a great collaboration with him.”

With Sligar contributing the expertise in chemistry and Schulten in biophysics, it's a team that looks ready to fulfill its goal. And that is just a starting point, Aksimentiev said.

“The other thing is detecting cell signals,” he said. “With nanopores, if we can sequence DNA, we can probably sequence everything the cell produces — rapidly, on a chip.”

So has this native of the Ukraine who has been all around the world found a niche with his research at Beckman?

“Absolutely. I feel this is the best place to be,” he said. “I will definitely be working in the area of bringing together silicon and bio-materials in terms of sensors, but also in terms of a means of communicating between those two — wet and dry. That is something that is just starting.”

This article is part of the Summer 2006 Synergy Issue, a publication of the Communications Office of the Beckman Institute.