Page 200 - An Introduction to Microelectromechanical Systems Engineering

DNA Analysis 179

Injection
+ −
Embedded channel 1

1 Glass plate Injected sample

2 2 4
4

3 Port 3

Separation
~ 700V
− +
1 Shorter
fragments
1
Fluid plug
2
2 4
4
Electrophoretic
separation
Separation channel
3 Injection channel 3
Figure 6.6 Illustration of the fluid injection and separation steps in a miniature DNA electropho-
resis system. An applied electric field electrophoretically pumps the fluid molecules from port 3 to
port 1 during the injection step. Another applied voltage between ports 2 and 4 initiates the
electrophoretic separation of the DNA molecules. The smearing of the fluid plug in the separation
channel is schematically illustrated. The capillary channels have a typical cross section of 8 × 50
2
µm . The separation capillary is 3.5 cm long. (After: [17, 18].)

injection-channel loading time is critical: If it is too short, more short DNA frag-
ments are injected in the next step; if it is too long, the sample is biased toward
longer fragments. Once the injection channel is filled, the applied voltage is
switched to be across the two ends of the separation channel. The applied electric
field directs the small “plug” of ionized fragments from the intersection of the two
channels into the separation channel. After a short injection time, the ends of the
injection channel are made positive to pull ionized fragments still in the injection
channel back from the junction with the separation channel; otherwise, injection
would occur continuously. At an applied electric field of 180 V/cm, it takes approxi-
mately 2 min to complete the separation of the DNA fragments in the injected plug.
This compares with 8 to 10 hours to complete an equivalent separation using con-
ventional gel electrophoresis or 1 to 2 hours with conventional capillary electropho-
resis. Optical imaging of a fluorescent tag on each DNA fragment is used to detect
the separated products inside the channel. The results from Woolley and Mathies
indicate a resolution of a single nucleotide in DNA strands that are up to 1,000
nucleotides long.
Though this demonstration is an important accomplishment, much remains to
be done before portable DNA sequencing instruments are available on the market.
A complete sequencing system must integrate PCR with electrophoresis—or some