PCR Thermal Cyclers Overview

The polymerase chain reaction, or PCR, is a ubiquitous laboratory technique of molecular biology to amplify a target DNA sequence to millions of copies. Since PCR technology relies on repeated thermal cycling for target amplification, the equipment to automate the process, thermal cyclers, may play a critical role in the success of experiments. This section covers the evolution and advancement of thermal cyclers over the years.

1. History of thermal cyclers in early days of PCR

At the inception of the technology in the early 1980s, DNA amplification by PCR was a time-consuming and laborious process. Thermal cycling steps were performed manually, involving repeated transfers of DNA samples among three large water baths set at different temperatures for denaturation, annealing, and extension. Since heat-stable DNA polymerases were not commonly available at the time, the enzyme had to be replenished after each round.

History of thermal cyclers in early days of PCR
Figure 1. The first commercial thermal cycler,
the TC1 DNA Thermal Cycler.

Therefore, engineers started to look into inventing an all-in-one instrument (thermal cycler) that would help automate the PCR process. The first automated machine developed, called "Mr. Cycle," resolved the need for manual addition of fresh enzyme after each cycle by using liquid handlers and water baths [1]. In 1987 the first commercial thermal cycler, the TC1 DNA Thermal Cycler from Perkin Elmer Cetus, became available with the ability to program heating and cooling of samples using a metal block (Figure 1). In 1988 the first use of a thermostable enzyme—Taq DNA polymerase—in PCR, using the TC1 thermal cycler, was reported [2]. This paved the way for applications of PCR in a wide range of scientific fields, as well as innovations in thermal cyclers that revolutionized molecular biology research.


2. Progress in thermal cyclers for advancement of PCR

Since the introduction of the TC1 thermal cycler, significant technical progress has been made on various features of equipment, to improve PCR experiments. 

a. Better sample handling

In the early development of thermal cyclers, the cooling system relied on a bulky plumbing compressor, which made it impossible to have a small-footprint instrument. In the present day, solid-state Peltier blocks are utilized in thermal cyclers to both heat and cool by controlling the direction of an electrical current (Figure 2). Advanced Peltier systems can heat and cool the block at a fast rate (e.g., 6°C per second), enabling fast PCR to complete more PCR runs in a day.

Basic principle of the Peltier block

Figure 2. Basic principle of the Peltier block. Heat may be generated or absorbed where two different materials (semiconductors in this case) connect, depending on the direction of an electrical current.

Similarly, a heated lid is now a common feature of thermal cyclers to prevent evaporation and condensation of PCR samples during runs. Prior to the introduction of the heated lid, samples were overlaid with mineral oil to achieve the same purpose. In addition to being inconvenient and messy, oil overlays limited the amount of a sample that could be used in downstream applications, because part of the sample had to be left behind to prevent carryover of the oil.

Likewise, many of today’s thermal cyclers are built with flexibility in sample throughput in mind. With interchangeable blocks, a benchtop thermal cycler may accommodate, for example, from one to 480,000 amplification reactions (Figure 3). For high-throughput automation, thermal cyclers designed for hands-free operations and integration with robotic liquid-handling platforms are now available.

Basic principle of the Peltier block
Figure 3. Interchangeable blocks of a thermal cycler for various throughputs.


b. More precise PCR optimization

Since annealing of primers to the target sequence is critical to obtaining successful PCR results, the temperature for the annealing step often requires optimization. To examine different temperatures simultaneously, gradient thermal blocks were developed, which are designed to enable setting desired low and high temperatures around the theoretical annealing point at the two ends of a single metal block (Figure 4A). “Better-than-gradient” technology is also now available, in which insulated separate metal blocks replace a single block (Figure 4B). This allows more precise temperature control for faster optimization [3].

Basic principle of the Peltier block
Figure 4. Thermal cycler blocks. (A) Gradient temperature control. (B) Applied Biosystems VeriFlex “better-than-gradient” temperature control.

Besides the block technology, algorithms to control sample temperatures have improved over the years. Complex mathematical models are applied for more precise regulation of block temperatures to achieve uniform heating and cooling of the PCR samples. This innovation involves measuring the temperature of the samples themselves, in addition to the temperature of the thermal block [4].


c. Faster PCR protocols

“Fast” PCR refers to protocols that dramatically speed up overall PCR run times (Figure 5), typically reducing run times from approximately 2 hours to less than 40 minutes, saving time and increasing throughput. Thermal cycler technologies that enable fast PCR include:

  • Advances in the Peltier elements for faster ramp rates, as well as heating and cooling of the block and samples
  • Improved algorithms to control and better predict sample temperatures [4]
Effects of ramp rates

Figure 5. Effects of ramp rates on: (A) duration of PCR cycling, and (B) total ramp time of a 30-cycle PCR. The following temperatures were used to calculate the ramp times: denaturation, 98°C; annealing, 60°C; extension, 72°C.  

These instrument improvements, along with innovations in PCR consumables and reagents such as ultrathin-walled low-profile PCR plastics and highly processive engineered DNA polymerases, have significantly enabled and improved fast PCR.


d. Easier PCR setup, enhanced accessibility

Thermal cyclers today are designed for easy programming of PCR protocols. PCR protocols often vary based on the DNA targets, primer sequences, DNA polymerases used, and experimental goals. Therefore, thermal cyclers that are equipped with intuitive user interfaces, such as touch screens and easy programming features, enable faster and more efficient protocol setup (Figure 6).

Recent advances also allow convenient access to thermal cyclers anytime and from anywhere, using a mobile device or desktop computer. Connectivity to the cloud offers enhanced accessibility at your fingertips and freedom to create and share protocols as well as to schedule, start/stop, and monitor PCR runs.


In summary, thermal cyclers have evolved in technology and design since their introduction in the 1980s. Innovations continue to facilitate improvement in PCR and advances in molecular biology research.