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RT-PCR Protocol

Reverse Transcription Polymerase Chain Reaction (RT-PCR) is a laboratory technique used in molecular biology to amplify a specific RNA segment. The process involves two key steps: reverse transcription, where RNA is converted into complementary DNA (cDNA) using an enzyme called reverse transcriptase, and PCR (Polymerase Chain Reaction), where the cDNA is amplified exponentially. This technique is crucial for applications such as gene expression analysis, diagnosis of infectious diseases, and cancer research.

RT-PCR Protocol Steps


RNA Extraction

RNA extraction is the first critical step in the RT-PCR workflow, involving the isolation of RNA from various sample types such as cells, tissues, or fluids. This process typically employs a combination of chemical and physical methods to lyse cells, inactivate RNases (enzymes that degrade RNA), and separate RNA from DNA, proteins, and other cellular components. The quality and purity of the extracted RNA are paramount, as contaminants can inhibit reverse transcription and PCR. The extracted RNA is then quantified and assessed for purity using spectrophotometry or fluorometry, ensuring it is suitable for the subsequent reverse transcription step.

Reverse Transcription

Reverse transcription is the process of converting RNA into complementary DNA (cDNA) using the enzyme reverse transcriptase. This step is crucial for converting the RNA’s message into a more stable DNA form, which can then be amplified using PCR. During this process, primers (either random hexamers, oligo-dT, or gene-specific primers) are used to initiate the synthesis of cDNA from the RNA template. The efficiency of this step is vital as it directly impacts the yield and quality of cDNA, which in turn affects the PCR amplification efficiency and accuracy.

PCR Amplification

PCR amplification involves the exponential amplification of the synthesized cDNA using specific primers and a DNA polymerase enzyme. This step begins with the denaturation of the double-stranded cDNA, followed by annealing of primers to specific target sequences and extension of these primers by the DNA polymerase to form new DNA strands. This cycle of denaturation, annealing, and extension is repeated multiple times (typically 25-40 cycles), exponentially increasing the number of copies of the target DNA. The choice of primers, DNA polymerase, and cycling conditions are critical factors that influence the specificity and efficiency of the amplification.

Product Detection

Product detection in RT-PCR involves analyzing the amplified product to confirm the presence and quantify the amount of the target sequence. This is often achieved using gel electrophoresis, where the amplified DNA is visualized as bands on a gel, or through real-time PCR (qPCR) methods, which allow for the quantification of DNA in real-time during the PCR process. In qPCR, fluorescent markers are used to label the DNA, and the increase in fluorescence is measured at each cycle, providing quantitative data on the amount of starting material. The choice of detection method depends on the specific requirements of the experiment, such as the need for quantification or only qualitative assessment.

Resource Spotlights

Opentrons helps you automate RT-PCR with open-source protocols for the OT-2 and Opentrons Flex

Distinct Methods of RT-PCR


Two-Step RT-PCR

In Two-Step RT-PCR, the reverse transcription of RNA into cDNA and the subsequent PCR amplification are performed in separate reactions. This approach offers a high degree of flexibility and sensitivity, making it particularly suitable for applications where precise quantification is crucial, such as in differential gene expression analysis or when working with very small quantities of RNA. Additionally, since the cDNA is synthesized in a separate reaction, it can be stored for future use or used in multiple PCR reactions to analyze different targets from the same RNA sample. This method is ideal for researchers who require a versatile tool for various experiments or those who may need to perform multiple analyses on a single RNA sample.

One-Step RT-PCR

One-Step RT-PCR, in contrast, combines the reverse transcription and PCR amplification into a single reaction mixture. This method is particularly advantageous for streamlining the workflow, reducing the total time required for the experiment. It is especially useful in diagnostic applications, such as in the detection of infectious diseases, where speed and reduction of contamination risk are critical. Researchers who prioritize efficiency and simplicity, particularly in a clinical or diagnostic setting, often opt for the one-step RT-PCR method.


Key Differences Between One-Step and Two-Step RT-PCR

RT-PCR has never been easier

The OT-2 is a bench-top liquid handler designed to be accessible and flexible enough to automate many common applications.

How to Automate the RT-PCR Protocol Process


Benefits of Automation over Manual Pipetting for RT-PCR Protocol


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