DNA and chips

The secret ingredient in a future biological computer is to add a little DNA. But, making hybrid devices from a silicon chip and a strand of genetic material means mixing hard-wired microelectronics technology with the softer world of molecular biology.

Now, chemists at the University of Newcastle upon Tyne have come up with a solution that could lead to new lab-on-a-chip devices and biological sensors for use in medicine and environmental analysis. It might even one day allow biology to compute or provide an interface between electronic devices and living things.

Ben Horrocks

Ben Horrocks

Newcastle chemists Benjamin Horrocks and Andrew Houlton and their colleagues have devised a way to automate the solid-phase synthesis of DNA on a semiconductor chip. They believe their method could readily be adapted to the conventional fabrication techniques of photolithography used in the microelectronics industry to pattern the microscopic transistors and circuitry on a computer chip.

The team recently reported how it has found a way to attach a DNA sequence of just seventeen nucleotides to a silicon surface modified with organic molecules. The key to unlocking hybrid DNA chips lies in the team’s use of bifunctional organic molecules. At one end the molecule has the right chemistry to allow it to be attached to an oxide-free silicon surface. The other end of the molecule has a functional chemical group on which a DNA strand can be grown using an automated DNA synthesizer of the kind found in biotech laboratories the world over.

Andrew Houlton

Andrew Houlton

The team is working with two aims in mind – first, the development of chemical sensors and secondly the synthesis of DNA on silicon surfaces for nanoscale molecular architecture. This addresses the projected reduction in the size of electronic components which by 2015 are predicted to be of the order of nanometres (i.e. built from molecules), explains Houlton.

Gel electrophoresis reveals DNA is attached to the silicon

Gel electrophoresis reveals DNA is attached to the silicon

Previous endeavours in this area have generally used glass in preference to silicon wafers and those that have focused on silicon have applied organic molecules to an oxidised surface rather than the naked silicon chip. The Newcastle team has now confirmed that it is possible to cover the surface of a silicon chip with DNA strands. Moreover, the 17-base DNA strands can be coupled with the complementary DNA strand making the familiar DNA double helix. From the nanodevice perspective the importance of the team’s work lies in their ability to pattern the surface of the silicon rather than simply randomly deposit DNA strands. Patterning using the printing and etching techniques of microelectronics fabrication means they can tightly control the arrangement of the DNA on the surface and so produce what might one day become molecular circuitry.

A DNA-patterned silicon surface

A DNA-patterned silicon surface

Sequential modification of a silicon surface with DNA

Sequential modification of a silicon surface with DNA

Further reading

Angew. Chem. Int. Ed., 41, 615 (2002)
http://www3.interscience.wiley.com/cgi-bin/abstract/90512278/ABSTRACT

DOI: 10.1002/1521-3773(20020215)41:4<615::AID-ANIE615>3.0.CO;2-Y

Benjamin Horrocks
http://www.ncl.ac.uk/chemistry/staff/profile/b.r.horrocks

Andrew Houlton
http://www.ncl.ac.uk/chemistry/staff/profile/andrew.houlton

Suggested searches

Molecular Electronics
Nanotechnology

Slip sliding away

Children playing on the beach are all too familiar with land slip and the devastating effects it and the waves it can produce on their shorelines sandcastles. But, when an oceanic volcano, such as Kilauea on Hawaii, undergoes a ‘flank collapse’, when the side of the volcano slips off into the ocean the resulting giant wave train created by the traumatic displacement of a great volume of water can have a savage impact on distant shores as a tsunami slams into a coastline.

Flank collapses involve great masses of rock – up to 5000 cubic kilometres by one estimate – and at their worst could make catastrophic and life-threatening tsunami, among the islands or even across thousands of nautical miles. Tsunami have long wave periods and so reach far inland once they hit a coast. Kilauea is constantly monitored for any rocky disturbances so that early warning of an outgoing tsunami can be made; the team also monitors for earthquakes and volcanic activity. Now, Peter Cervelli of Stanford University in California and his team believe they have unearthed a phenomenon that may be involved with flank collapse.

Cervelli in traditional Hawaiian garb setting up a GPS monitor

Cervelli in traditional Hawaiian garb setting up a GPS monitor

The researchers observed over a period of three days in November 2000 a slipping of the flank of Kilauea by some 9 centimetres. Interestingly, this was at a time when there was no seismic rumbling (geologists’ standard signal of rock movement). They report in Nature that this movement was preceded by unusually heavy rainfall, and they speculate that it may have been the heavy rains that triggered the movement as the region’s water table changed.

This 9 cm slip is very small compared with a full-blown flank collapse of the size needed to produce a tsunami but the Stanford team reckon their findings suggest that geoscientists need to monitor risky volcanoes with Global Positioning System (GPS) instruments that can spot movements even when there is no conventional seismic activity.

Simulated tsunami waves following a volcanic flank collapse

Simulated tsunami waves following a volcanic flank collapse

Steven Ward of the University of California in Santa Cruz points out that the geological record tells us that mountain ranges have been built and then washed down to the sea; that entire ocean basins have opened and closed like a door, so it should be of no surprise that on the geological timescale volcanic islands are but dust on the wind. He adds, in the same issue of the journal, that oceanic volcanoes usually grow too steep to support their entire mass and slough off flank material.

GPS in position

GPS in position

Sonar has revealed this to be true for most volcanic island chains. The Hawaiian Islands have seen seventy flank collapses in the past 20 million years. The last one was just a few hundred thousand years ago, although there seems to be one flank collapse somewhere on the globe approximately every 10,000 years.

The small slippage observed by Cervelli and his team suggests that Kilauea may in for a bigger shock in the near future. The near future to an earth scientist though might be another few millennia or even millions of years. But, as children soon learn shoreline sandcastles are fragile at the best of times. Kilauea could be due for a full-blown flank collapse, which with several thousand cubic kilometres of rock involved would be equivalent to Majorca or Rhode Island shifting tens of kilometres sideways.

Ward is convinced that the Cervelli work is not simply due to signal noise. For me, their map of a dozen GPS displacement arrows all pointing out to sea far beyond their error ellipses tells the whole story, he says, What else can they indicate but some early stage of one of those flank collapses that litter the geological record? A 2,000 cubic km piece of Hawaii is slip-sliding away.

Cervelli and his team hope that their ongoing studies will provide early warning for the Hawaiian islanders and for those distant shores that might lie in the path of a tsunami.

Further reading

Nature, 415, 1014 (2002)

Steven Ward
http://es.ucsc.edu/personnel/Ward/index.html

Suggested searches

Flank Collapse
Landslides
Volcanoes
Tsunami

Planetary shortlist

There is a bright disc of interplanetary dust particles that surrounds our solar system, starting beyond the orbit of Saturn and stretching beyond the outer reaches, according to European astronomers. The discovery could lead to a speedier way of determining whether distant stars have their own planets too.

Markus Landgraf of the European Space Agency and colleagues have obtained the first direct evidence of a bright dust disc surrounding our Solar System and they reckon it should help illuminate the search for planets orbiting other stars in our galaxy. The finding will help mission planners short list stellar candidates for observation with ESA’s future planet-search missions, Eddington and Darwin.

Markus Landgraf

Markus Landgraf

Planetary systems are thought to condense from a cloud of gas and dust. Planets form near the central star, where the material is densest. However, at great distances from the star, the gas and dust is sparse and can coalesce only into a vast band of small, icy bodies. A dust ring would therefore seem indicative of a mature star with a planetary system. In our Solar System, the dust particles that reach out beyond the orbit of Neptune form the Edgeworth-Kuiper belt. The dust is continually lost to deeper space though and according to Landgraf there has to be something to replenish it for the disk to be maintained. Indeed, 50 tonnes of dust have to be produced every second.

If you have a dust disc around a star that’s not particularly young, then it’s extremely interesting because the dust has to come from somewhere. The only explanation is that the star has planets, comets, asteroids or other bodies that collide and generate the dust, explains ESA’s Malcolm Fridlund.

Traces of the disc surrounding our Solar System are visible in this image taken by COBE. The blue band curving across this image is created by the dust disc surrounding our Solar System (Copyright Michael Hauser (Space Telescope Science Institute)

Traces of the disc surrounding our Solar System are visible in this image taken by COBE. The blue band curving across this image is created by the dust disc surrounding our Solar System (Copyright Michael Hauser (Space Telescope Science Institute)

To prove the existence of the dust disk, Landgraf and colleagues sieved vast quantities of NASA’s Pioneer 10 and 11 data from the 1970s and early 1980s. These spacecraft found dust particles of unknown origin beyond Saturn’s orbit. It was initially suggested that the dust might come from comets but these objects only discard dust when they are close to the sun, they are frozen solid beyond Saturn. They compared the size of the dust particles from beyond Saturn with those measured by ESA’s Ulysses spacecraft, which has orbited the poles of the Sun for more than a decade.

Artist’s impression of Pioneer’s Jovian fly-by

Artist’s impression of Pioneer’s Jovian fly-by

The interstellar grains detected by Ulysses are typically ten to a hundred times smaller than the smallest grain that could be detected by Pioneer. Thus, the Pioneer grains have to be made somewhere within our Solar System.

The only plausible origin is collisions between the small, icy objects in the Edgeworth-Kuiper belt. Since these are the remnants of planet formation, the team believe that planetary systems around other stars will also produce constantly replenishing dust rings.

Brightly shining discs around the stars Vega and Epsilon Eridani have already been observed and the ESA results hint that these discs are evidence of their planets. If we see a similar dust ring around a main sequence star (a mature star, like the Sun), we’ll know it must have asteroids or comets. If we see gaps in the dust ring, it will probably have planets which are trapping the dust grains in resonant orbits, or ejecting them from the Solar System during close encounters, explains Landgraf.

The results appear in the May 2002 issue of The Astronomical Journal

Further reading

Suggested searches

Interplanetary Dust Particles
Extrasolar Planets