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PCR Instruments Buying Guide

How to Choose a PCR Instrument

A PCR instrument, also known as a thermal cycler, performs the polymerase chain reaction (PCR) by precisely, rapidly, and repeatedly changing temperatures to drive the biochemical amplification process.

Before purchasing a PCR machine, it’s important to clarify your experimental goals. Do you need to perform quantitative analysis of template DNA, and how high is the required quantification accuracy? Do you need gradient functionality or any other special features?

1. PCR principle

2. Types of PCR Instruments

3. Gradient PCR

4. Other Special Features

5. Related Instruments

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PCR principle

— Denaturation / Annealing / Extension

DNA consists of two complementary strands forming a double helix, following the “base pairing principle.” Once the base sequence of one strand is known, the complementary strand can be replicated accordingly. Based on this principle, a specific DNA fragment can be amplified through three main steps:

Denaturation

At a high temperature of around 95°C, the template DNA denatures as the hydrogen bonds between the two strands break, resulting in single-stranded DNA.

Annealing

At a lower temperature (usually 50°C–65°C), numerous forward and reverse primers (short single-stranded DNA fragments) bind to the single-stranded DNA, marking the start and end points of the region to be copied.

Extension

The temperature is raised to the optimal working temperature of about 72°C. DNA polymerase extends the new strand from the primers by synthesizing complementary DNA in the (5'-3') direction.

Types of PCR Instruments

According to quantification principles and application scenarios, PCR can be classified into Conventional PCR, Real-Time Quantitative PCR (qPCR), and Digital PCR (dPCR).

Conventional PCR

The primary purpose of conventional PCR is to amplify DNA, without providing any quantitative feedback. The amplified products are analyzed using gel electrophoresis, and qualitative or semi-quantitative results are obtained based on the presence and brightness of the DNA bands.

Quantitative PCR (qPCR)

During each amplification cycle, the fluorescence signal intensity is monitored in real time, reflecting the concentration of the amplified product. By measuring the number of cycles required for the fluorescence signal to reach a defined threshold (Ct value), the initial quantity of the template DNA can be indirectly estimated.

Digital PCR (dPCR)

dPCR directly quantifies the initial amount of template DNA. The PCR reaction mixture is partitioned into tens of thousands of microreactors, each containing either zero or one target molecule. After amplification, the number of “positive” (with signal) and “negative” (without signal) reactions is counted, and the absolute copy number of the target DNA is calculated using the Poisson distribution formula.

Feature	PCR	qPCR	dPCR
Quantification capability	Qualitative / Semi-quantitative	Relative / Absolute quantification	Absolute quantification
Basis of quantification	Band intensity of final product	Ct value	Ratio of positive microdroplets
Need for standard curve	No	Yes (for absolute quantification)	No
Accuracy and sensitivity	Low	High	Extremely high
Output results	DNA bands (gel electrophoresis image)	Amplification curve, melting curve, Ct value, concentration	Droplet scatter plot, absolute copy number concentration

Gradient PCR

By setting different temperature gradients across the same heating block, Gradient PCR allows users to determine the optimal annealing temperature in a single run. This gradient function can be equipped on all three types of PCR instruments mentioned above.

The optimal annealing temperature for primer-template binding is theoretically calculated during primer design, but it may differ from the actual best temperature. The temperature that produces the brightest and most specific target band—with the weakest or no background bands—is considered the optimal annealing temperature.

Other Special Features

Interchangeable Modules

Allows users to manually replace the sample block (module) inside the instrument according to experimental needs. (Not applicable to dPCR.)

Heated Lid

Provides heating to the top of the reaction tube cap, preventing the reaction mixture from evaporating or condensing on the lid during high-temperature cycles.

Fast Heating and Cooling

Refers to the instrument’s maximum heating and cooling rate.

For other special feature requirements, contact us !