Physics professor Henk Postma has proposed a way of sequencing a DNA strand without blasting or computer processing

(October 30, 2008)

Oct 30, 2008

Graphene could accelerate genomics

The “wonder material” graphene could soon be used
to analyse DNA at a record-breaking pace. That’s the claim of a
physicist in the US who has proposed a new way of reading the sequence
of chemical bases in a DNA strand by sending the molecule through a
tiny slit in a graphene sheet.

While the technique has yet to be verified experimentally, if
successful it could be eligible for the $10 million X Prize for
Genomics, which has set the challenge of developing a new rapid and
low-cost sequencing technology.

The genetic profile — or “genome” — of an organism is determined by
recording the full sequence of acid base pairs that make up its DNA. In
2003, the Human Genome Project made history by determining the entire
human genetic code — 3 billion DNA base pairs that took 13 years to
analyse using a technique that has changed very little since the late
1970s.

This “shotgun” approach first isolates a DNA strand and forces it to
copy itself millions of times over in a chemical reaction. These are
then “blasted” into tiny fragments because current techniques for
sequence reading can detectors can only analyse very short sections of
DNA. Finally, a supercomputer matches up overlapping base patterns to
piece together the full genome.

No processing required
Now, Henk Postma at California State University Northridge has proposed
a way of sequencing an entire DNA strand without the need for blasting
or computer processing (arXiv:0810.3035).

The technique involves cutting a very narrow slit or “nanogap” along
the length of a piece of graphene — an extremely strong sheet of carbon
just one atom thick. A voltage is applied perpendicular to the
graphene’s surface, which causes the DNA strand to pass slowly through
the slit one base at a time.

A second voltage is applied across slit and electrons are able to
“tunnel” across the nanogap via the base that happens to be passing
through the slit. There are four different types of base in a DNA
molecule, and each should support a different tunnelling current —
allowing the base type to be identified.

While the idea of sequencing DNA by sending it through a tiny gap is
not new, previous schemes had relied on using separate materials for
the membrane and electrodes — and aligning the two materials has proved
to be a considerable challenge. Postma’s design gets around this
problem by having the graphene function as both membrane and electrode.

Postma believes that detector could be made from a graphene sheet
sandwiched between glass plates that are held together by van der Waals
forces.

Technology should be possible
According to Changgu Lee, a mechanical engineer at Colombia University,
some of the technology to realize Postma’s design may be available
already. “Creating the nanogaps in graphene was demonstrated this year
using both STM [scanning tunnelling microscopy] and catalytic cutting
with metal particles”, he said.

Postma says that traditional sequencing techniques are limited to
determining about 800 base pairs per recording. By contrast, he
estimates his design could yield 100,000 bases per recording, and if
run continuously it would read the whole human genome in two and a half
hours. He also believes that his technique could lead to sequencing
devices that are smaller and cheaper than existing systems.

If successful, Postma’s system could be a contender for the X Prize for
Genomics, which aims to award $10m to the inventor of a device that can
sequence 100 human genomes within 10 days or less,to a specified
accuracy and costing no more than $10,000 per genome.

Postma said he is continuing to develop his design, but added: “I
published the paper to get feedback from the scientific community, in
the open, because I believe that will lead to the best possible
technology.”

And it seems DNA experts are ready for a new technology. Geoffrey
Baldwin, a molecular biologist from Imperial College in the UK said “to
truly develop health care we need the profile of 100s of genomes not
just the few we have at the moment”. He added “there is now a great
opportunity for a new technique to become the standard in base
sequencing”.

About the author

James Dacey is a science journalist based in the UK

Publication: Nanotechweb.org