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Real-Time PCR vs. Traditional PCR

Real-Time PCR—also called quantitative polymerase chain reaction (qPCR)—is one of the most powerful and sensitive gene analysis techniques available and is used for a broad range of applications including quantitative gene expression analysis, genotyping, SNP analysis, pathogen detection, drug target validation and for measuring RNA interference. Frequently, real-time polymerase chain reaction is combined with reverse transcription to quantify messenger RNA (mRNA) and MicroRNA (miRNA) in cells or tissues.

As the name suggests, real-time PCR measures PCR amplification as it occurs. This completely revolutionizes the way one approaches PCR-based quantitation of DNA and RNA. In traditional PCR, results are collected after the reaction is complete, making it impossible to determine the starting concentration of nucleic acid.

Real-Time PCR vs. Traditional PCR at a Glance
  Real-Time PCR Traditional PCR
Overview
Measures PCR amplification as it occurs. Measures the amount of accumulated PCR product at the end of the PCR cycles.
Quantitative? Yes, because data is collected during the exponential growth (log) phase of PCR when the quantity of the PCR product is directly proportional to the amount of template nucleic acid. No, though comparing the intensity of the amplified band on a gel to standards of a known concentration can give you 'semi-quantitative' results.
Applications
  • Quantitation of Gene Expression
  • Microarray Verification
  • Quality Control and Assay Validation
  • Pathogen detection
  • SNP Genotyping
  • Copy Number Variation
  • MicroRNA Analysis
  • Viral Quantitation
  • siRNA/RNAi experiments

Amplification of DNA for:

  • Sequencing
  • Genotyping
  • Cloning
Summary Adavantages of Real-Time PCR
  • Increased dynamic range of detection
  • No post-PCR processing
  • Detection is capable down to a 2-fold change
  • Collects data in the exponential growth phase of PCR
  • An increase in reporter fluorescent signal is directly proportional to the number of amplicons generated
  • The cleaved probe provides a permanent record amplification of an amplicon
 Disadvantages of Traditional PCR
  • Poor Precision
  • Low sensitivity
  • Short dynamic range < 2 logs
  • Low resolution
  • Non-Automated
  • Size-based discrimination only
  • Results are not expressed as numbers
  • Ethidium bromide for staining is not very quantitative
  • Post-PCR processing


Phases of a PCR Reaction
To understand why traditional PCR is limiting, it is important to understand what happens during a PCR reaction. A basic PCR run can be broken up into three phases:

  • Exponential
    Exact doubling of product is accumulating at every cycle (assuming 100% reaction efficiency). The reaction is very specific and precise. Exponential amplification occurs because all of the reagents are fresh and available, the kinetics of the reaction push the reaction to favor doubling of amplicon.

  • Linear (High Variability)
    As the reaction progresses, some of the reagents are being consumed as a result of amplification. The reactions start to slow down and the PCR product is no longer being doubled at each cycle.

  • Plateau (End-Point: Gel detection for traditional methods)
    The reaction has stopped, no more products are being made and if left long enough, the PCR products will begin to degrade. Each tube or reaction will plateau at a different point, due to the different reaction kinetics for each sample. These differences can be seen in the plateau phase. The plateau phase is where traditional PCR takes its measurement, also known as end-point detection.
Figure 1:
PCR Phases
Phases of PCR Reaction

Traditional PCR Measures at the Plateau, Giving You Variable Results
In Figure 2, three replicate samples, which had same amount of DNA in the beginning of the reaction, have different quantities of PCR product by the plateau phase of the reaction (due to variations in reaction kinetics). Therefore, it will be more precise to take measurements during the exponential phase, where the replicate samples are amplifying exponentially.

Figure 2:
Identical Samples Produce Different Quantities of
Reaction Product by the Plateau Phase of PCR
Phases of PCR Reaction

 

Real-Time PCR Measures at the Exponential Phase for More Accurate Quantitation
Real-Time PCR focuses on the exponential phase because it provides the most precise and accurate data for quantitation. Within the exponential phase, the real-time PCR instrument calculates two values. The Threshold line is the level of detection at which a reaction reaches a fluorescent intensity above background. The PCR cycle at which the sample reaches this level is called the Cycle Threshold, Ct. The Ct value is used in downstream quantitation or presence/absence detection. By comparing the Ct values of samples of unknown concentration with a series of standards, the amount of template DNA in an unknown reaction can be accurately determined.

Figure 3:
The PCR cycle at which the sample reaches a fluorescent
intensity above background is the Cycle Threshold or Ct
Phases of PCR Reaction

 

TaqMan® Probe- and SYBR® Green-Based Detection
Every real-time PCR reaction contains a fluorescent reporter molecule—a TaqMan® Probe or SYBR® Green dye, for example—to monitor the accumulation of PCR product. As the quantity of target amplicon increases, so does the amount of fluorescence emitted from the fluorophore.

Figure 4:
Advantages of Real-Time PCR vs. Traditional PCR
Phases of PCR Reaction

Applied Biosystems Has a Full Range of Real-Time PCR Products for Routine and Challenging Applications
Applied Biosystems offers a comprehensive set of products for real-time PCR-based gene expression, miRNA, copy number variation, and SNP genotyping analysis: from off-the-shelf gene-specific probe and primer sets, to everyday reagents and plastics, instrument systems, software, and everything in between.

View our real-time PCR Products >