Microfluidic Tools for DNA Analysis - DNA Nanotechnology: From Structure to Function - page 112

7.2.1 Amplification

In the past decades, various miniaturization strategies were proposed for nucleic
acid amplification. Since the most popular type of assay for nucleic acid is
polymerase chain reaction (PCR), miniaturization has to deal with how to cycle
the reactants between different temperatures required by PCR. Due to the distinct
isothermal advantage, isothermal amplifications have also been integrated into
microfluidic chips. Amplifications can be performed in a liquid solution or on a
surface: homogeneous reaction (e.g., normal PCR in a tube) and heterogeneous
reaction (e.g., solid-phase amplification).

7.2.1.1 Thermal Control

PCR is carried out at different temperatures to realize denaturing, annealing,
and extension, in turn. The miniaturization of the PCR devices has been widely
reported. The core component in the PCR device is the temperature controller
which was commercialized as a thermocycler or many other heating blocks that
should be in physical contact with the PCR vessel, and the large thermal mass
of the traditional heating blocks itself restricted the efficiency of thermal cycling.
Landers and coworkers developed infrared radiation as a noncontact heating method
combined with effective cooling by compressed air for rapid thermal cycling in
small volumes [ 3 , 4 ]. This approach can be easily applied to microfluidic chips for
qualitative or quantitative DNA analysis [ 5 - 7 ], where the heating/cooling sources
are independent from the chip. Optical heating enabled a fast heating rate due to
the selective absorption of the infrared laser by PCR buffer only, and the power of
the infrared laser can be alternated between different levels to achieve each desired
temperature [ 7 ].
Beyond the noncontact heating scheme, the most typical solution for a rapid
amplification was devised in 1998, reported by Manz et al. [ 8 ]. Under the con-
sideration of “space-for-time”, they sacrificed some space and simultaneously set
three temperature zones to carry out three reactions (i.e., denaturing, annealing, and
extension, respectively). They controlled the timing for each step by controlling
the length of the flow path and controlled the cycle number by using a serpentine
microfluidic channel that transverses the different zones of temperature (Fig. 7.1 ).
It gets rid of complicated temperature controls, thus simplifying the design and
reducing the cost both in time and money, while increased cost in space is in fact
very small because of the miniaturized microfluidic design.
Even though this design is a great advancement for miniaturized on-chip PCR,
some problems still remain, such as the limited cycle number, the sizable dimension,
and the heavy external equipments, which became the issues resolved by the follow-
up studies. Henceforth, on-chip PCRs have been widely developed, and many
interesting alternatives for fluid control in small scales have been proposed. To
reduce the dimension of the device, Chen and coworkers designed a reciprocating