Sequencing technology holds great promise as a tool for diagnosing disease pathogens and identifying tissue from the DNA they contain. If the challenging technological barriers can be overcome, then some day we will see handheld devices that can rapidly identify DNA sequences from tissue samples and the environment.
This is the view of a team from the University of Washington (UW) in Seattle that has developed a technique involving "nanopore DNA sequencing" that overcomes a significant technological barrier to advancing sequencing technology. The researchers describe their new technique in a paper published in the journal Nature Biotechnology.
The project leader is Jen Gundlach, a UW professor of physics. Lead author Andrew Laszlo, a graduate student in Prof. Gundlach's lab says one of the reasons scientists get excited about nanopore DNA sequencing is they believe it could one day lead to handheld medical scanners reminiscent of the multifunction "tricorders" used by Starfleet personnel in the fictional Star Trek universe to rapidly detect pathogens or diagnose genetic disorders on the spot.
Key step is ability to identify long sequences of DNA
The UW team's new nanopore-based technique is important because most of the current technology used in gene sequencing can only work with short sequences of DNA - typically snippets of no more than 50 to 100 of the four nucleotides or "letters" that make up the genetic code, namely the molecules adenine, guanine, cytosine and thymine. Plus, they have to be processed by large sequencing devices in a lab, and it can take days to weeks until the result are ready.
But nanopore technology promises to transform this and make DNA sequencing technology cheaper and faster, and - now with the step the UW team has taken - also able to deal with longer DNA sequences.
The technology exploits a natural phenomenon found in bacteria whose membranes contain tiny tunnel-like structures that allow them to control the flow of nutrients in and out of their cells.
Nanopore has aperture just big enough for single strand of DNA to pass through
For their study, the UW team used a genetically altered bacterial pore that has a diameter of around one nanometer - or 1 billionth of a meter - at its narrowest point, hence the expression "nanopore." Such an aperture is just large enough to allow a single strand of DNA to pass through, one nucleotide at a time.
Illustration of a nanopore derived from a genetically modified bacterial membrane channel being used to sequence DNA.
Image credit: Ian Derrington
A DNA nanopore sequencer has a nanopore channel between two salt solutions that with the help of voltage applied to it, forces ions to pass through the channel. The resulting electrical current can then be measured. But when a strand of DNA passes through the channel it changes the current by interfering with the smooth flow of the ions. The amount of interference depends on which of the four nucleotides is inside the nanopore at the time.
Such technology was first proposed 20 years ago, and scientists hoped it would quickly lead to a faster, cheaper alternative to gene sequencing. But their efforts to reach such a holy grail were plagued with problems - mostly to do with accurately identifying the nucleotides as they passed through the nanopore. Sometimes a nucleotide is missed, or read more than once, yielding an imprecise readout of a DNA sequence.
But the UW team found a way to bypass the problem. Their solution was in two parts. The first part was to identify the electronic signature - the unique pattern of changes in electrical current in the nanopore - produced when each of the 256 different combinations of the four nucleotides passed through the nanopore.
The second part was to match the electronic signatures generated when a segment of DNA passed through the nanopore with those expected from known DNA sequences of genes and genomes stored in a database. A match would show that the particular DNA sequence passing through the nanopore was close to or the same as one in the database.
First time nanopores have generated interpretable signatures of long DNA sequences
They tested their method by using the nanopore sequencer to read the genetic code of a bacteria-infecting virus called bacteriophage Phi X 174, which is often used to test new genome sequencers. They found their nanopore system was able reliably to read sequences as long as 4,500 nucleotides from the virus' genetic code.
Co-author Jay Shendure, UW associate professor of genome sciences, who describes the achievement as "a major step forward," says it is the "first time anyone has shown that nanopores can be used to generate interpretable signatures corresponding to very long DNA sequences from real-world genomes."
Because it relies on matching patterns to known sequences, the technology can only be used to identify already sequenced genes and genomes - it cannot identify newly discovered ones, but the team is confident it is only a matter of time before a new version can do that.
Funds from the National Institutes of Health, National Human Genome Research Institutes, and the National Science Foundation helped finance the project.
Meanwhile, in July 2013, Medical News Today learned how researchers in Switzerland developed a quick test for bacteria using nano-sized "tuning forks" that could cut the timescale for identifying the cause of bacterial infections to minutes instead of days. Such a test could save lives by making sure patients with serious infections get the right antibiotic straight away.
Written by Catharine Paddock PhD