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PCR Applications Guide

Overview of PCR
The PCR process includes several steps: denaturation where DNA strands are melted and separated, annealing where the primers anneal to template DNA, and extension where the enzyme works to elongate the DNA strands.  These steps are carried out 20-35 times in a thermal cycler to produce many replicates of the DNA template.  PCR is highly efficient and specific, generating over 10 million copies of target DNA from just a few molecules.  Because the PCR process is so sensitive and specific, it is important to choose high quality PCR products to produce optimal results.

Since the introduction of our first thermal cycler in 1987, we have continued to develop and support new PCR instruments and reagents to advance molecular biology research. Today we offer a variety of thermal cyclers with features that suit a range of research needs. We offer special chemistries and thermal cyclers that enable researchers to speed up this process, delivering results in just a third of the time.  From thermal cyclers, enzymes, dNTPs, and plastics to award-winning service, Applied Biosystems offers you what you need for PCR success.

Find Your Application

We have all of the PCR products you need for wherever your applications take you. Find your application below and see which thermal cyclers, enzymes, dNTPs, and plastics we recommend for your research.



  Application Recommended Enzymes Compatible Thermal Cyclers
Cloning PCR is the preferred method to obtain a higher abundance of target DNA to clone. Downstream applications using high-purity cloned genes include:
  • cDNA library construction
  • Gene family characterization
  • Large-scale genome mapping using YACs/ BACs
Expression Analysis Use RT-PCR to convert RNA into cDNA, then amplify the cDNA. Applications include:
  • Rapid amplification of cDNA ends (RACE) to amplify unknown cDNA
  • Differential display PCR
  • Detection of rare transcripts
  • Quantitative gene expression
Genotyping Use PCR to study differences in DNA sequences. Related applications include:
  • Allele-specific PCR
  • Fragment-length polymorphism analysis
  • Haplotyping
  • Linking emulsion PCR
  • SNP analysis
  • Microsatellite studies
Mutagenesis Use PCR to perform site and random mutagenesis for:
  • Protein, RNA, and DNA structure-function relationships
  • Protein engineering
  • Adding unique restriction sites
  • DNA shuffling and library construction
Sequencing Use direct (noncloning) sequencing for:
  • Mutation detection
  • Candidate gene analysis
  • Genetic linkage studies
  • Evolutionary studies
  • Genome (gap filling and shotgun) sequencing
  • Primer walking
Bacterial Gene Amplification Use PCR to analyze bacterial genomes—vital for antibiotic and vaccine development. Also useful for:
  • Pathogen detection
  • Amplified fragmentlength polymorphism (AFLP) analysis used in comparative bacterial genomics
Viral Gene Amplification PCR assays are a highly sensitive, specific, and fast means of detecting viruses for:
  • Nucleic acid sequencebased amplification (NASBA)
  • Pathogen detection
Fast PCR PCR can be performed faster for unique PCR screening applications. Such applications include:
  • High-throughput screening
  • Colony PCR library screening
  • Rapid genotyping of transgenic animals
Long PCR (5-20 kb) An enzyme blend efficiently amplifies larger targets for:
  • Sequence mapping
  • Mitochondrial genome PCR
  • Gene cluster studies
  • cDNA cloning of long transcripts
Multiplex PCR Use multiplex PCR to amplify many targets in a single tube. This method provides target-specific amplification with primers specific for each target. Used for:
  • Human identification studies
  • Variable number of tandem repeats (VNTR) screenin


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