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How to Choose the Right Gradient PCR for Your Lab?

Views: 551     Author: Site Editor     Publish Time: 2023-02-24      Origin: Site

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Gradient PCR is not an actual type of PCR. It is a variant of the conventional PCR that makes it easier to optimize PCR reactions by pinpointing the precise annealing temperature. The PCR allows for the amplification of an infinite number of amplicons, or copies of the gene of interest, which are then used in the subsequent molecular application.

Further applications include diagnosing inherited diseases, evolutionary research, phylogenetic analysis, and DNA barcoding. However, the primary goal of PCR is to amplify the DNA effectively, precisely, and with a high yield. Additionally, the sensitivity and specificity of any PCR reaction are essential.

To achieve our goals, the reaction must be optimized utilizing temperature changes, MgCl2, a buffer, and various cyclic conditions. This guide will discuss how you can choose the right gradient PCR for your lab.

What Is Gradient PCR?

The gradient PCR machine can use several optimization experiments in one run to accurately determine the annealing temperature. The gradient PCR can also determine the annealing temperature and other things, such as the ideal concentration of MgCl2, buffer, and primers. The gradient PCR machine has the same structural components as a conventional PCR. It consists of a power button, display, upper heating lid, and lower heating block.

The PCR can alter the temperature quickly. It changes between each step in a split second. The gradient PCR machine's lower heating block differs from a regular PCR. Its lower heating block has a different heating column. It contains 12 columns, each pair of columns having another heating block. Temperature changes between each pair of heating blocks of >0.5°C and 5°C are possible.

However, the temperature of each row stays the same as that of the corresponding columns. As a result, the power of gradient PCR allows us to analyze six alternative annealing temperatures for a PCR reaction in a short time.

Gradient PCR solutions: Four E's Scientific's PC Optima 96

Gradient PCR Optima 96 is a product of Four E's Scientific. This machine combines three separate PCR machines into one, making it more than just a gradient PCR machine. We can always run three separate protocols on this PCR equipment. Additionally, three of every grid have a gradient platform, allowing even greater optimization in a single experiment.

It offers temperature control for PCR optimization because it's six independent temperature blocks. This machine has a faster heating and cooling rate with a USB for gradient PCR protocol export and import.

What Is the Difference Between Conventional PCR and Gradient PCR?

The major difference between a conventional PCR and a gradient PCR is that conventional only has a single heating unit and transports a single temperature across thewell. On the other hand,  gradient PCR has multiple temperature zones in several pairs of columns. It has about six heating units, which implies that six annealing temperatures are distributed across the wells.

What Are the Advantages of Gradient PCR Over Conventional PCR?

The main advantage of Four E's Scientific gradient PCR over conventional PCR is that it is fast. For scientists that use polymerase chain reaction (PCR) for sequencing, cloning, genotyping, mutagenesis, and a variety of other uses, gradient PCR is a crucial piece of lab equipment. It has an accurate PCR annealing temperature gradient that simplifies PCR assays in a single run.

Conventional PCR takes time because it only has one heating block. Gradient PCR determined the optimal annealing temperature with the least number of steps.

Why Use Gradient PCR?

You need to use gradient PCR to enhance PCR reactions. PCR amplification involves using  the gradient in PCR to determine the ideal annealing temperature. The gradient is a variant of the standard PCR that makes it easier to optimize the PCR process by pinpointing the precise annealing temperature.

The gradient PCR machine can be used to conduct a number of optimization tests in a single run to accurately determine the annealing temperature. It can also be used for several purposes

Things to Consider When Choosing Gradient PCR

These are some of the things to consider when choosing gradient PCR:

1. Temperatures that Are Precise and Constant Throughout the Thermal Block

Because the three primary PCR processes are temperature-dependent, the precision of a thermal cycler's temperature may influence whether a PCR is successful or unsuccessful. To produce accurate and repeatable PCR findings, well-to-well constancy of the temperature across a thermal block is essential. The thermal cycler utilized must achieve the desired temperature as precisely and uniformly as possible across the block.

Regular testing with a temperature verification kit and recalibrating by a qualified expert as necessary are two methods to enable thermal precision.

2. Precise Temperature Control for Optimization of Primer Annealing

One characteristic of a thermal cycler that helps with the optimization of primer annealing in PCR is gradient temperature control. To evaluate multiple temperatures simultaneously for ideal primer annealing, the gradient setting aims to achieve changing temperatures across the block, typically at a 2°C increment or decrement in each lane.

A real gradient, in theory, would show linear temperatures throughout the block. Gradient thermal cyclers, on the other hand, are typically built with just one thermal block, whose temperature is managed by just two heating and cooling elements, one at each end.

3. Achieving Accurate Sample Temperatures: Ramp Rate, Hold Time,

and Algorithms

For PCR experiments to be accurate and effective, a thermal cycler must be able to manage sample temperatures accurately. Precise management of sample temperatures depends on instrument-specific factors, including ramp rate, hold time, and algorithms to anticipate sample temperatures.

The ramp rate of a thermal cycler, often reported in degrees Celsius per second (°C/sec), represents the shift in temperature from one PCR step to another over time. The heating and cooling of thermal blocks are referred to as "up ramp" and "down the ramp," respectively.The samples undergo a slower ramp rate (than the block) because it takes time for thermal energy to be transferred from the block to the pieces. Therefore, it is essential to distinguish between and comprehend the following definitions of ramp rates:

● The fastest temperature variations that the block can achieve throughout a short time during the ramp are defined as the maximum or peak block ramp rate.

● A more accurate way to gauge a thermal cycler's speed is to use the average block ramp rate, which measures the rate of temperature change over a longer time.

● Actual temperatures attained by the samples are reflected by the maximum sample ramp rate and average sample ramp rate. The performance of a heat cycler and its possible impact on PCR can therefore be more accurately compared using sample ramp rates.


Amplification is a time-consuming and expensive operation. Therefore, high-end optimization is crucial for lowering costs and saving time. The PCR gradient makes the amplification easy by

saving time, reagents, and consumables. The need for extra PCR or reagent is satisfied by the temperature-dependent optimization. Get one of Four E’s Scientific Gradient PCRtoday and get started.

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