Researchers from Boston University and the University of Massachusetts Medical School recently made a significant advancement in what promises to be a viable competitor to third-generation sequencing technology. The team, led by Amit Meller, an associate professor at BU, demonstrated the first implementation of perforated silicon chips, or solid-state nanopores, as a reliable and accurate method for the identification of roughly 200 bases per second. Unlike previous nanopore-based sequencing methods that use an electrical signal readout, this new method employs an optical signal readout using high-speed digital camera technology.
The team converted target DNA to a binary code that is then identified by molecular beacons with two types of fluorophores. A series of photo bursts are then detected as the nanopores are used to sequentially strip off the beacons at a rapid rate. The optical imaging approach allows for a straightforward readout from a large amount of nanopores -simultaneously. "Our method permits very high capture rates of single, long DNA molecules into the nanopores at low sample concentrations," Meller says. "This directly drives throughput and allows for very small sample amounts, and we have proven that we can control those capture rates experimentally in our recent paper." Their work was recently published in Nano Letters.
Meller and his colleagues say that nanopore sequencing technology will enable the realization of extremely high-throughput DNA sequencing, eventually allowing for rapid high-quality human genome sequencing. It will also afford researchers the ability to analyze extremely long DNA molecules for diagnostic purposes, when whole-genome resequencing isn't necessary.
"With these capabilities, scientists will be better equipped to perform genome-wide comparative studies of human diseases such as cancer, revealing the genetic variations associated with a specific cell's conditions," Meller says. "These types of pioneering studies, which have already begun to emerge using second-generation DNA sequencing methods, will become faster and more affordable. Moreover, the potential ability of nanopores to analyze extremely long DNA molecules will allow genomicists to explore long-range genomic rearrangements at the single genome level — a feat that is currently challenging."