Biochemical Engineering Project

Title : Biotechnology on a Chip

1. What is a biochip?

Definition : Biochips are similar to semiconductors, instead of having electronic circuits and they have biological material such as DNA, RNA or other protein, attached to the surface of a "chip," which can be glass, plastic or silicon.

Function : Biochips are to identify which genes in a cell are active at any given time and how they respond to changes. This allows physicians to determine what genes might be the cause of a particular disease and provides researchers for designing drugs for treatment.

Type : There are two main types of biochips, depending on the material attached. One is Nucleic acid biochip which has DNA or RNA and the other is protein biochip. There is another type of biochip, called a lab chip, which uses microfluidics to do many of the standard lab tests that are applied in hospitals today. In this project, DNA chip will be mostly focused because it has the hottest market demands.

Table.1 Electronic Business(April 2000) gives the following market for biochips, in millions of US dollars:

Year	DNA Chip	Lab Chip	Protein Chip	Total
1999	$158	$14	$4	$176
2001	$249	$35	$8	$292
2005	$745	$157	$68	$950

Figure 1. DNA chip Figure 2. Protein chip

DNA chip : DNA (Deoxyribonucleic acid) is double-stranded and it has a nucleoside base (adenine, cytosine, guanine or thymine), a ribose sugar and a phosphate group. Transcription is done by copying the DNA’s instructions to RNA,specifically messenger RNA (mRNA). The mRNA then translates the DNA "message" into protein by the aid of tRNA. The process is summarized below:

DNA transcription \ mRNA translation \ proteins

· View animation of beginning of transcription

· View animation of transcription from start to finish

· View animation of initiation of translation

· View animation of elongation of translation

· View animation of termination of translation

Nucleic acid biochips are used to identify unknown DNA or RNA (nucleic acid strand) via the process of hybridization—or bonding—between an unknown nucleic acid strand and a known nucleic acid strand.

This is done by first denaturing the unknown DNA with heat, which melts the bonds between the two strands of DNA, producing single-stranded DNA. Then the unknown DNA or RNA is taken over a biochip, which has single-stranded DNA or RNA attached to its surface. If one of DNA or RNA pieces on the biochip is complementary to the unknown DNA / RNA, then hybridization will occur and a fluorescence is given off that makes a researcher know the DNA or RNA matched the unknown DNA.

Quick Time video is linked to help understanding of concept and processing of biochips.

· Biochips for Gene Research Part 1: Concepts

· Biochips for Gene Research Part 2: Mechanics

Biochip Devices : Interest in biochips started in the 1980s when the idea of constructing electronic devices made out of protein molecules was first seen to be a reality. Research showed that these biodevices could be made on the molecular level. This decreased the scale of integration of integrated circuits by several orders of magnitude, thus increasing the memory of the computer by a factor of 10 to 100 million. The first idea of miniaturizing these circuits involved printing them on thin silicon wafers. This is called lithography. However, it was discovered that there was a limit to the size that a silicon wafer could be made and still be able to function as an electronic circuit. This proposed an absolute limit on the possible size of a circuit. After this "silicon wall" was reached, attention was turned to the electron flow between molecules, as opposed to the larger silicon crystals. This would allow the circuits to be miniaturized even further (Kaminima, 1991).

2. The application of biochips.

Pharmaceutical Research

They discover new Currently pharmaceutical company is the only market for biochips. They discover new drugs. In new drug research, biochips are used in drug assays and in toxicology, where the biochips can test the toxicity of new drugs. So animal testing is not necessary to test. Packard BioScience company

Disease Diagnostics

Biochips are being tested to identify mutated genes that can lead cancer, Alzheimer’s and other diseases. Currently, biochips cannot be used for disease diagnostics because they have not been cleared by the FDA. It will take several years to be used regularly for disease diagnostics. Related web-site

Crime detection

NA testing in high profile criminal cases has been on the news quite a bit over the last few years. DNA testing is a good standard for determining guilt or innocence of a suspect. In other words, it makes possible far more accurate tests for crime analysis. The process for analysis usually takes a couple of weeks, and there is always concern of DNA cross-contamination at the testing facility, or within the police evidence room. There would be less delay and less handling of the material with less potential for errors and contamination. Related articles

Biochips in Water and Environmental Testing

Using biochips as highly sensitive detectors for microbial or organic pollution, they can enable the identification of natural enzymes to be used to detoxify chemical digest pollutants and to clean up contaminated soil and water. Some of them are already being used to test the water supply in Atlanta, Georgia. Biochips are also used as part of the Department of Defense’s biological warfare response.

Biochips and Transplantation

Biochips could be used to precisely match donors and recipients to alleviate the rejection of transplanted organs.

3. Company research of biochips

There are many companies working in the biochip field. The market leader in biochips is Affymetrix which is a combinatorial chemistry company. When Affymax was bought by Glaxo Wellcome in 1995, it was the only company with commercially available biochips, although many other companies were close to commercialization having beta-test products in the field.

Other companies are working exclusively on biochips. For example, Nanogen, Hyseq, Genometrix, Packard Instrument Company, Oxford Gene Technology and etc. These are just the best known of the companies. Because of the large potential of biochips, new companies show up every month. Some large, well-known electronic companies are also working in this field, including Motorola, Hitachi and Samsung.

4. A specific Example of biochip

The contents are based on the paper, “Silicon Wafer integrated enzyme reactors” Biosensors & Bioelectronics 10 (1995) 289-299

Enzyme reactors were fabricated on silicon wafers using microstructure technology. Two types of reactors were fabricated by etching silicon wafer and compare which type has more enzyme activity.

These reactors were made of several parallel vertically-cut flow channels as seen in Figure 3. Reactors with two different channel densities were fabricated such as 10 channels/mm, 165 mm deep( Type B): and 25 channels/mm, 235 mm deep ( Type A ).

Figure 3. Two types of reactor design, showing different etch depth and lamella frequency

Type A Type B

The etching was performed in KOH solution at 80^oC on a silicon wafer and

Pyrex glass lid seal the reactor to complete the flow-through cell ( Figure 4).

A glass/silicon bond was made by heating to 450^oC and applying 1000 V across the glass/silicon interface.

Figure 4. A reactor view

For next step, glucose oxidase was immobilized on the reactors. Heating during bonding between silicon and glass generates a thin oxide layer and he oxide layer is used as the coupling site of enzyme immobilization. Their corresponding enzyme ( glucose oxidase ) activities were determined by pumping through Trindler reagent which contains glucose at various flow rates. The result was shown in the Figure 5.

Figure 5. Linear fit and Lineweaver Burk plot of glucose oxidase reaction rate

+ : Type A reactor

D : Type B reactor

As shown in the Figure 5, Type A reactor has better performance because it has larger surface area to react. A reactor surface area increase of 3 times resulted in a proportional enzyme activity increase in the reactor. The maximum glucose reaction rate for the reactor with 25 channels/mm was approximately 17 mM.

Reference

1. Speculation Press – Weird Science

http://www.speculationpress.com/weirdsci.htm

2. Argonne Biotechnology Research – Biochip Technology

http://www.ipd.anl.gov/biotech/programs/biochip/

3. Biochip

http://www.faw.uni-ulm.de/deutsch/bereiche/autonomsys/biochip/indexeng.html

4. ARCS - Homepage

http://www.arcs.ac.at/L/LB/biochip/home

5. Institute of Microelectronics – MEMS - Biochip

http://www.ime.org.sg/mems/mems_biochip.htm

6. Biochip, NYT

http://linkage.rockefeller.edu/wli/news/biochip_nyt99.html

7. “Silicon Wafer integrated enzyme reactors”

Biosensors & Bioelectronics 10 (1995) 289-299