Page 201 - An Introduction to Microelectromechanical Systems Engineering

180 MEMS Applications in Life Sciences

other DNA detection method—as well as include all fluid preparation and handling
functions, such as pumping, valving, filtering, mixing of reagents, and rinsing. This
demands the development of a complete system with many enabling technologies,
MEMS being only one of them.
The electrophoresis part of the DNA sequencing process has been commercial-
ized by companies such as Caliper Life Sciences, Inc., of Hopkinton, Massachu-
setts, with the product now being sold as the LabChip by Agilent Technologies. Up
to 12 samples containing variable-length sections of DNA are placed in the dispos-
able LabChip, which is inserted into the Agilent 2100 Bioanalyzer system for analy-
sis. This system is about the size of a small suitcase, has a separate computer for
control and data acquisition, and is powered by a wall outlet, making the system
semiportable.
The entire LabChip structure is made of sheets of glass. Patterning of glasses is
limited to usually photolithography and etching or laser ablation (see Chapter 3).
The layers are bonded together under heat and pressure, then cut apart. The use of
glass in a simple process leads to low cost, making a single use before disposal
economical. Single-use devices have the advantages of no concern about cross con-
tamination from previous samples, greatly reduced chances of clogging, and no
long-term risk of material degradation with use. Many glasses (and plastics) are
transparent to visible and UV light, which is useful in optical detection schemes.
Some specifications for the Agilent DNA 1000 LabChip include a DNA concentra-
tion range of 0.5–50 ng/µl, a sizing range of 25–1,000 base pairs, a sizing accuracy
of ±15%, and a resolution better than 10% over most of the range [19]. The sample
volume is 1 µl and takes 30 min to analyze.

DNA Hybridization Arrays
Once fragments of an unknown DNA sample have been amplified into many copies,
they can be read with DNA hybridization arrays. These are different sequences of
preassembled nucleotides attached to a substrate (see Figure 6.7). The DNA sections
to be identified, with lengths in the range of a hundred to thousands of bases, are
tagged with a fluorescent dye at one end. When placed in a buffer solution on the
substrate, sections of some of the unknowns hybridize to the complementary
sequences on the substrate. As discussed earlier, hybridization is the process by
which DNA strands match up and bind with complementary DNA capture probes.
The substrate is then rinsed and illuminated. The locations of fluorescence indicate
where hybridization occurred and thus which sequences are present in the unknown.
This approach is particularly beneficial in the detection of specific gene mutations
and in the search for known pathogens.
Several companies commercially produce microscale DNA arrays. One of

the market-leading products is the GeneChip from Affymetrix of Santa Clara,
California [20]. The GeneChip is produced on 5-inch square fused quartz substrates,
which are coated with a bonding layer comprised of molecules to which the DNA
nucleotides can adhere, followed by a protection group [21, 22]. Using a standard
photolithographic mask (see Chapter 3), ultraviolet light is shone through 20-µm
square openings to remove the protection groups, activating selected sites on the
substrate (see Figure 6.8). A solution containing one type of nucleotide (A, T, G,
or C) with a removable protection group is flushed across the surface. These