Hardware Reference
In-Depth Information
Chapter 5
Optimization of On-Chip Polymerase
Chain Reaction
5.1
Introduction
The amount of Deoxyribonucleic acid (DNA) strands available in the biological
sample is a major limitation for many genomic bioanalyses [
1
-
4
]. For example, in
the study of gene dosage in tumor DNA by comparative genomic hybridization,
the analysis procedure requires several hundred nanograms of DNA strands for
fluorescent labeling [
2
]. It is difficult to obtain such a large amount of DNA strands
directly from biological samples. To overcome this problem, the polymerase chain
reaction (PCR) technique is used as the first step for these bioanalyses to amplify
(replicate) the initial DNA strands [
2
,
3
,
5
]. Based on the categories of operations
involved, the procedure of genomic analysis can be divided into three separate
stages [
6
]. The first stage is sample preparation for PCR; the second stage is
amplification of the DNA strands; after DNA amplification, the third stage includes
the subsequent operations, such as mixing the droplet that contains DNA strands
with other reagent droplets, detecting the concentration of intermediate product
droplets, and the hybridization of the amplified DNA sequences [
4
].
Digital microfluidic biochips (DMFBs) are used extensively for the quantitative
analysis of biomolecular interactions and they offer a viable platform for performing
the three stages of the PCR procedure on the same chip layout [
3
]. On a DMFB,
nanoliter or picoliter-scale droplets can be manipulated by a two-dimensional
electrode array using the electrowetting-on-dielectric effect [
3
,
7
,
8
]. With sensors
(such as photodetectors and a fluorescent microscope) integrated in the microfluidic
system, precise control for droplet volume as well as the reaction time for each step
in the experiment can be achieved [
3
,
9
]. Compared to conventional instruments and
analyzers, the DMFB platform offers several advantages for implementing PCR. It
can implement the complete PCR procedure seamlessly, and achieve low reagent
consumption, short time-to-results, rapid heating/cooling rates, and integration of
multiple processing modules [
5
,
10
]. The size and power consumption of the entire
PCR system can also be reduced.
