|
Researchers have devised a nanoscale sensor to electronically
read the sequence of a single DNA molecule, a technique that is fast and
inexpensive and could make DNA sequencing widely available.
The technique could lead to affordable personalized medicine,
potentially revealing predispositions for afflictions such as cancer, diabetes,
or addiction.
“There is a clear path to a workable, easily produced
sequencing platform,” said Jens Gundlach, a University of Washington
physics professor who leads the research team. “We augmented a protein
nanopore we developed for this purpose with a molecular motor that moves a DNA
strand through the pore a nucleotide at a time.”
The researchers previously reported creating the nanopore by
genetically engineering a protein pore from a mycobacterium. The nanopore, from
Mycobacterium smegmatis porin A, has
an opening 1 billionth of a meter in size, just large enough for a single DNA
strand to pass through.
To make it work as a reader, the nanopore was placed in a
membrane surrounded by potassium-chloride solution, with a small voltage
applied to create an ion current flowing through the nanopore. The electrical
signature changes depending on the type of nucleotide traveling through the
nanopore. Each type of DNA nucleotide—cytosine, guanine, adenine, and thymine—produces
a distinctive signature.
The researchers attached a molecular motor, taken from an
enzyme associated with replication of a virus, to pull the DNA strand through
the nanopore reader. The motor was first used in a similar effort by
researchers at the University of California, Santa
Cruz, but they used a different pore that could not
distinguish the different nucleotide types.
Gundlach is the corresponding author of a paper published
online in Nature Biotechnology that
reports a successful demonstration of the new technique using six different
strands of DNA. The results corresponded to the already known DNA sequence of
the strands, which had readable regions 42 to 53 nucleotides long.
“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,” Gundlach said.
Gundlach said the nanopore technique also can be used to
identify how DNA is modified in a given individual. Such modifications,
referred to as epigenetic DNA modifications, take place as chemical reactions
within cells and are underlying causes of various conditions.
“Epigenetic modifications are rather important for things
like cancer,” he said. Being able to provide DNA sequencing that can
identify epigenetic changes “is one of the charms of the nanopore
sequencing method.”
