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A Gene Platform on Silicon

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DQI Bureau
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Despite the millions of components that a Pentium-class ‘chip’ now packs, the integrated circuit is not quite as integrated as it could be. Amidst that maze of circuitry, transistors and passive devices such as resistors, what’s missing from the silicon is the photonics. Most light sources (such as LEDs) and light sensors use other compounds such as gallium arsenide, because of the poor optical properties of silicon. And so they’re on separate devices, making them expensive, or unfeasible.

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Let there be Light
Integrating the active electronics along with sensors, fluid-transport channels and other diverse elements onto a single silicon chip draws on several areas of research at STMicroelectronics. Silicon is normally not used for light emitting devices or photosensors, because of poor optical properties. At the atomic level, silicon has an “indirect band-gap” that inhibits efficient light emission. That’s why LEDs use “III-V compounds” like gallium arsenide (so called because their elements belong to groups III and V of the Periodic Table of Elements). That means using separate devices outside the silicon chip. 



Solution: Change the optical properties of silicon by doping it with ions of lanthanide or rare earth elements (there are 14 of them, and each emits light at a specific frequency). Similarly, photo-detectors are built into the silicon chip. All this allows, for instance, a complete opto-coupler to be integrated into the same silicon wafer. Up ahead, there are cheaper, advanced displays using a poly-silicon active matrix and organic light emitters. And STMicroelectronics engineers are busy building a laser into that same chip of silicon.

But silicon can be changed. It can be doped with specific ‘impurities’ that alter its optical properties. This brings a whole range of light-based ‘elements’ onto the silicon chip, opening up a range of possibilities. That’s one of the things European semiconductor technology company STMicroelectronics has been working on in its labs.

In its facilities in the serene Mediterranean island of Sicily in south Italy, this company has produced a silicon chip with micro arrays that support on-chip DNA analysis at the genetic level. When DNA from diseased and healthy sources is added to the silicon, it becomes a platform for genetic research into the cause of diseases. This Gene Platform is a monolithic (one-chip) array that includes the sensing and supporting electronics, and

photonics.

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A media group taken to the town of Catania in Sicily in September was shown a machine placing droplets containing DNA precisely onto the silicon. Through a scanner, computer and software, we then saw the array of color dots representing healthy gene pairs and those that were likely candidates for specific diseases.

The array of tiny dots on a silicon surface allow genetic researchers to accurately place a single polynucleotide strand of the twin-strand, double-helix DNA from individuals with specific diseases (the target DNA) along with a strand of healthy DNA as reference (the probe). The objective is to find out the precise difference between the two DNA strands, thus identifying the genes that could be responsible for the disease. 

Like a lock and key, the two strands will come together completely if the specific deoxyribose and phosphate groups are complementary, forming strong covalent (chemical) bonds. If there is a difference, that pair will not form the bond, showing up as a different color. One end of the DNA strand itself forms a covalent bond with the silicon, anchoring it firmly in place.

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The chromatically marked DNA fluoresces when excited by electrons, and this can be detected by photo-sensors. Different colors indicate whether the genes have paired correctly or not, and therefore whether they are identical or different. 

The micro-array on ST Microelectronics’ Gene Platform allows the monitoring of expressions of 10,000 or more genes at a time. And the single piece of silicon contains the active electronics, photonics–and remarkably, even the micro-channels transporting the DNA fluid, all integrated into one piece of silicon, making such analysis quicker and cheaper. (Capillary forces in the micro-channels transport the solution carrying the DNA.)

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Photo-receptor elements on the chip detect the fluorescence and color of the DNA just above it. Thus, adding optical functions to silicon helps allow active DNA analysis within a silicon chip, and the integrated electronics in the same silicon senses and communicates the color changes in the DNA pairs in the array. Using silicon for the base substrate for the DNA analysis also has other advantages–mainly, a great benefit in signal to noise ratio. Glass itself would fluoresce, so such background noise from glass would have to be “subtracted” from the results of such an experiment.

Parallel with the silicon biosensor array development is ongoing research into DNA strands to explore genetic pairs as alternative memories, including research on organisms that change state or color after absorbing a photon, making them candidates for future ‘optical storage’.

Piezo-based system dispenses DNA-laden fluid onto a micro-array on a silicon chip.

(Piezo-electric dispensers carved out of silicon also transfer ink from inkjet cartridges to paper, which is why HP is one of

STMicroelectronics’ major customers)
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While yet at the research and testing stage, ST officials say they expect to manufacture the Gene Platform biosensors in a year for “simple stuff” and in three years for “more complex stuff”.

The $6.3 billion STMicroelectronics is the fourth-largest semiconductor company in the world. Headquartered in Geneva, Switzerland, ST has three regional headquarters in Dallas, Texas (USA), Singapore (Asia-Pacific) and Tokyo (Japan). It has 17 manufacturing sites across the world including Catania in Italy, the US, and elsewhere. It is particularly strong in “system-on-chip” technology, and supplies chips to, inter al, Alcatel, Nokia, Philips, Siemens and Sony, inkjet print-heads to HP, and automotive electronics systems to DaimlerChrysler and Ford.

The ST group was formed in 1987 after the merger of SGS of Italy with Thomson of France. In May 1998, the company changed its name from SGS-Thomson Microelectronics to STMicroelectronics. Today, it has 43,000 employees (including over 1,000 in its India development center in Noida, UP), 16 R&D units and 39 design and application centers. The company is NYSE-listed (“STM”) since 1995.

Prasanto K Roy in Sicily (South Italy). The author was hosted by STMicroelectronics

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