Tiny DNA reader heralds fast cheap sequencing

The prospect of affordable personalized medicine using "genome sequencing while you wait" was brought a step closer this week when a study led by a University of Washington physics professor showed how a tiny nanoscale sensor can read the sequence of a single DNA molecule in a way that promises to be cheap and quick. Such a technique could make DNA sequencing more widely available, allowing personalized medicine to help individuals discover if they are susceptible to cancer, diabetes, addiction, and other diseases with genetic risk factors. Jens Gundlach, who describes himself as an experimental physicist with interests in fundamental physics and biophysics, and colleagues, write about their work in the 26 March online issue of Nature Biotechnology. They describe how, by attaching a molecular motor to a protein nanopore aperture, they managed to get a DNA strand to move through the pore one nucleotide at a time, allowing them to read the tiny characteristic ionic currents of each nucleotide, in a manner reminiscent of the old ticker tape machines used for reading information transmitted down telegraph lines. Gundlach told the media their work shows a "clear path to a workable, easily produced sequencing platform". In their paper, the team describe using the new nanopore technique to correctly identify six already known DNA sequences ranging from 42 to 53 nucleotides in length. They had already genetically engineered the protein nanopore from a bacterium called Mycobacterium smegmatis porin A (MspA), which has an aperture about 1 billionth of a metre in size, just big enough to allow a single strand of DNA to pass through. They enclosed the MspA pore in a lipid bilayer membrane and bathed the whole in potassium chloride. Applying a voltage to the membrane creates an ion current that flows through the protein pore so that when molecules pass through the aperture, they generate a small but detectable, change in current. The idea of nanopore technology to bring in faster, cheaper DNA sequencing (it cuts down the number of steps needed, for example when reading a person's genome), is not new. There are many private and academic research centers working on it. But what makes this system different is it allows the DNA strand to be pulled through one nucloetide at a time, at a pace slow enough to identify each of the four DNA nucleotides, cytosine, guanine, adenine or thymine, from its characteristic ion current signature. Previous systems have not been able to distinguish between the four different nucleotides. "The motor pulls the strand through the pore at a manageable speed of tens of milliseconds per nucleotide, which is slow enough to be able to read the current signal." The team made the motor from a virus-replication enzyme called bacteriophage DNA polymerase (DNAP) phi29. Researchers at the University of California, Santa Cruz had tried a motor using this enzyme, but they used a different pore that could not distinguish the nucleotides. The team suggest the technique could be used to spot epigenetic changes in DNA. Epigenetic changes are important for things like cancer: they show how the instructions held in DNA can be expressed differently in cells. The ability to spot epigenetic changes "is one of the charms of the nanopore sequencing method," said Gundlach. A program run by the National Human Genome Research Institute (NHGRI) helped fund the research. The program aims to find a way to sequence individual DNA for less than $1,000. Grundlach said the field was "moving fast". When the NHGRI program began, the cost of an individual DNA sequence would have been in six figures. Now, "with techniques like this it might get down to a 10-dollar or 15-minute genome project," he said.