Bioer GeneQ Thermal Cycler, Manual, Page: 8 / 33

Gene Q Thermal Cycler Chapter 1 Introduction
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3 PCR Thermal Cyclers
A PCR thermal cycler is a key device throughout the PCR experiment. Its performance determines
the accuracy of the experimental results. Its parameters, such as temperature keeping and
temperature ramp rate, play an extremely important role in DNA denaturation, annealing and
extension.
Chief Specifications of a PCR Thermal Cycler:
Temperature display
accuracy The bias between display temperature and practical temperature,
directly affects the quality of DNA annealing, elongation, and
denaturation, and should be reduced to an accepted level;
Heating/Cooling Rate Higher cooling/heating rate can greatly decrease the experimental time
and maintain the enzyme’s activity;
Temperature
Uniformity Excellent temperature uniformity guarantees consistent amplification
conditions for the same batch of reaction samples and then avoids
false positive or negative of the results caused by mismatched
operating conditions;
Temperature Control
Accuracy Higher temperature control accuracy ensures temperature stability
during the PCR amplification reaction, and therefore increase the
reliability of the experimental results;
Intelligent Degree More intelligent thermal cycler means less labor intensity for test
personnel and ensures the whole PCR reaction to be accomplished
successfully.
4 Common PCR Thermal Cyclers
a) Gradient Water Bath Thermal Cyclers
A gradient water bath thermal cycler consists of three water baths operating at different
temperatures. An automatic mechanical manipulator soaks the sample tube containing reactants in
the three water baths cyclically, and thus finishes the three processes of denaturation, annealing
and extension.
This device has high temperature control accuracy, high heating/cooling rate, and excellent
temperature uniformity. However, its intelligent level is very low, and it cannot accomplish some
relatively complex PCR processes. There are other disadvantages associated with this type of
thermal cycler, such as liquid evaporation in the bath, lack of the soak mode, inability of long-term
operation without human interference, temperature fluctuation caused when the sample tube is put
into the bath during heating/cooling process, and last but not least, the pollution issue. As a result,
this kind of thermal cycler has gradually been abandoned in the market.
b) Compressor Cooling Thermal Cyclers
At the center of a compressor cooling thermal cycler is located a block made of good conduction
material (aluminum or silver), over which several conical holes are distributed. Each of the conical
holes has the same shape as a standard microcentrifugal tube to ensure good contact between the
two. The resistance heater on the block’s outside bottom is responsible for block heating, whereas
the compressor takes charge of block cooling. Controlling the heater and compressor with a
microcomputer completes the required heating, cooling, and temperature keeping processes.
This device has much higher intelligent level and smaller size compared to a gradient water bath
thermal cycler. Nevertheless, the compressor’s inertia not only limits the cooling rate (to about
1
℃
/sec), but also increases the temperature undershoot. Moreover, there exists temperature
gradient over the block near the inlet and outlet of the compressor’s evaporation pipe (lower
temperature near the inlet area and higher temperature near the outlet area).