Scientists may soon have a cheaper alternative to current methods of DNA sequencing, thanks to new research by Professor of Physics Xinsheng Sean Ling and his group published in July's issue of Nanotechnology.
‘The team has shown that solid-state nanopores — very thin membranes with holes — can be used to detect regions of double-stranded DNA on a molecule consisting mostly of single-stranded DNA — a development that will eventually lead to an easier method of DNA sequencing.
This research is "related to an ongoing worldwide effort to develop nanopore sequencing," Ling said.
According to Ling, the Sanger method of DNA sequencing, which is the current, widely used DNA sequencing procedure, has its own procedural difficulties and can be expensive.
While taking a sabbatical in 2002, Ling became involved with the research, which he said is new and different from previous work he has done.
Ling's group, including Senior Research Associate in Physics Venkat Balagurusamy and Paul Weinger GS, has been able to use nanopores to detect the location of a 12-base-pair-long segment of double-stranded DNA surrounded on both sides by segments of single-stranded DNA, called a 12-mer.
Balagurusamy said that a nanopore is an "ultra-thin membrane with a small hole." When a molecule of DNA passes through the nanopore, the electrical current drops in comparison to the current measured when there is no DNA going through the nanopore.
"If DNA blocks the pore, you get a signal," he said.
According to Balagurusamy, because the diameter of single-stranded DNA is much smaller than the diameter of double-stranded DNA, the drop in current when each of these types of DNA passes through the nanopore will be different. This allows for the discrimination of double- and single-stranded regions of a DNA molecule passing through a nanopore.
Ling's group is therefore able to detect locations of hybridization, a complex process used to identify the presence of certain DNA sequences.
"With this positional information of hybridization, one should be able to sequence the whole genome," Ling wrote in an e-mail to The Herald.
Ling said his group would ultimately like to be able to detect a six-mer of double-stranded DNA, a feat that has not yet been achieved.
A six-mer of double-stranded DNA "is not stable at room temperature," Ling said. "We need to build a new experimental setup" in order to detect a six-mer, he added.
Balagurusamy said the ability to detect a six-mer of double-stranded DNA would be more beneficial for nanopore DNA sequencing than would the ability to detect a 12-mer, which Ling's group has recently achieved. Before Ling's group detected a double-stranded 12-mer, researchers had not been able to detect double-stranded DNA sequences of under about 1,000 base pairs among single-stranded sequences using nanopores, Balagurusamy said.
