Boston University biomedical engineers say they have devised a method for making genome sequencing faster and cheaper by significantly reducing the amount of DNA required. Doing so, they say, eliminates the expensive, time-consuming, and error-prone step of DNA amplification.

 

The study, published in the online edition of Nature Nanotechnology, details the work in detecting DNA molecules as they pass through silicon nanopores. The technique uses electrical fields to feed long strands of DNA through four-nanometer-wide pores, much like threading a needle. The method uses sensitive electrical current measurements to detect single DNA molecules as they pass through the nanopores.

 

“The current study shows that we can detect a much smaller amount of DNA sample than previously reported,” says Boston University Biomedical Engineering Associate Professor Amit Meller, who led the study. “When people start to implement genome sequencing or genome profiling using nanopores, they could use our nanopore capture approach to greatly reduce the number of copies used in those measurements.”

 

Currently, genome sequencing utilizes DNA amplification to make billions of molecular copies in order to produce a sample large enough to be analyzed. In addition to the time and cost DNA amplification entails, some of the molecules – like photocopies of photocopies – come out less than perfect. Meller and his colleagues at BU, New York University and Bar-Ilan University in Israel have harnessed electrical fields surrounding the mouths of the nanopores to attract long, negatively charged strands of DNA and slide them through the nanopore where the DNA sequence can be detected. Since the DNA is drawn to the nanopores from a distance, far fewer copies of the molecule are needed.

 

Before creating this new method, the team had to develop an understanding of electro-physics at the nanoscale, where the rules that govern the larger world don't necessarily apply. They made a counterintuitive discovery: the longer the DNA strand, the more quickly it found the pore opening.

 

“That's really surprising,” Meller says. “You'd expect that if you have a longer ‘spaghetti,’ then finding the end would be much harder. At the same time this discovery means that the nanopore system is optimized for the detection of long DNA strands – tens of thousands of basepairs, or even more. This could dramatically speed future genomic sequencing by allowing analysis of a long DNA strand in one swipe, rather than having to assemble results from many short snippets.”

 

Meller says DNA amplification technologies limit DNA molecule length to under a thousand basepairs. “Because our method avoids amplification, it not only reduces the cost, time and error rate of DNA replication techniques,” he says, “but also enables the analysis of very long strands of DNA, much longer than current limitations.”