Nanoscale DNA Sequencing Could Trigger Transformation in Personal Healthcare

In experiments with potentially far-ranging healthcare implications, a research team has devised a method that works at a very small scale to sequence DNA rapidly and comparatively inexpensively. That could create new opportunities for more effective individualized medicine, for example, providing blueprints of genetic predispositions for specific conditions and diseases such as cancer, diabetes, or addiction.

"The hope is that in 10 years people will have all their DNA sequenced, and this will lead to personalized, predictive medicine,” said Dr. Jens Gundlach, a University of Washington (UW; Seattle, USA) physics professor and lead author of a paper describing the new technique published the week of August 16, 2010, in the Proceedings of the [U.S.] National Academy of Sciences (PNAS).

The technique creates a DNA reader that combines biology and nanotechnology emplying a nanopore taken from Mycobacterium smegmatis porin A. The nanopore has an opening one billionth of a meter in size, just large enough to measure a single strand of DNA as it passes through. The scientists placed the pore in a membrane surrounded by potassium-chloride solution. A small voltage was applied to create an ion current flowing through the nanopore, and the current's electrical signature altered depending on the nucleotides traveling through the nanopore. Each of the nucleotides that are the basis of DNA-- cytosine, guanine, adenine, and thymine--generated a distinguishing signature.

The investigators had to solve two major hurdles. One was to create a short and narrow opening just large enough to allow a single strand of DNA to pass through the nanopore and for only a single DNA molecule to be in the opening at any time. Dr. Michael Niederweis, from the University of Alabama at Birmingham (USA), engineered the M. smegmatis bacterium to produce a suitable pore.

The second problem, according to Dr. Gundlach, was that the nucleotides flowed through the nanopore at a rate of one every millionth of a second, far too fast to sort out the signal from each DNA molecule. To compensate, the researchers attached a section of double-stranded DNA between each nucleotide they wanted to measure. The second strand would briefly catch on the edge of the nanopore, stopping the flow of DNA long enough for the single nucleotide to be held within the nanopore DNA reader. After a few milliseconds, the double-stranded section would separate and the DNA flow continued until another double strand was encountered, allowing the next nucleotide to be read.

The delay, although measured in thousandths of a second, is long enough to read the electrical signals from the target nucleotides, according to Dr. Gundlach. "We can practically read the DNA sequence from an oscilloscope trace,” he said.

The work was funded by the U.S. National Institutes of Health and its National Human Genome Research Institute (Bethesda, MD, USA) as part of a program to create technology to sequence a human genome for US$1,000 or less. That program began in 2004, when it cost approximately $10 million to sequence a human-sized genome.

The new research, according to the scientists, is a key step toward achieving DNA sequencing at a cost of $1,000 or less. "Our experiments outline a novel and fundamentally very simple sequencing technology that we hope can now be expanded into a mechanized process,” Dr. Gundlach concluded.

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University of Washington
University of Alabama at Birmingham