Biochips – fundamentals and applications - Electrochemical Sensors, Biosensors and Their Biomedical Applications - page 308

TABLE 11.2
A summary of the different array generation approaches

Spatial resolution Cost Probe length Ease of use

Robotic Poorest Most cost Not restricted Requires cloning

microprinting effective and PCR steps

Photolithography Highest Highest as expensive Limited to 25-mers Photolithography

equipments and or less method is

particular expertise protected by patent

are required and currently only

Affymetrix has the

rights to use this

method

Inkjet printing In between robotic In between robotic 5-75-mers Equipments need

printing and printing and strict maintenance

photolithography photolithography and experiment

must be performed

in a clean and

uncontaminated

environment

different level of hybridizations; due to this, the effects of cross-contaminations and
immobilization errors must be kept to a minimum. Therefore, a good resolution of the
DNA immobilization techniques is necessary for arraying and miniaturization.
A quick summary of each approach is listed in Table 11.2 and each of these methods
of creating the DNA arrays will be discussed in greater details in the subsequent chapters.

11.2.2.1 Fabrication by robotic microprinting (direct-deposition approach)
Most robotic microprinting systems make use of the XYZ coordinate motion control to
enable the printhead to move in all three directions. The printhead consists of a series of
pins as shown in Fig. 11.1. These pins are dipped into a tray of probe solution consisting
of pre-synthesized oligonucleotides or PCR products. The probe solution at the tip of
the pins is then transferred to a predetermined position on a solid substrate such as nylon
or glass slides. The amount transferred is typically in the range of nanoliter or picoliter
and is dependent on the geometry of the printhead. Cheung et al. [9] have reported that
with a DNA concentration of 2

µ g/ µ l, the spot size from the microprinting is approxi-

mately 100-150 µ m in diameter. These spots must be placed very close together (less

than 200 m apart) without overlapping each other. This is a challenge as machines with

high accuracy and fi ne resolution must be used to deliver these spots onto the substrate.
The nylon or glass substrate on which the probe solution is deposited must be pre-
treated with coupling agents such as lysine or acrylamide functional groups. Coupling
agents bind the probe cDNA to the substrate. After hybridization, the array is washed in
heated isopropanol and water to remove any unhybridized sample DNA. It is essential

µ