What are the different kinds of PCR?

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What are the different kinds of PCR?

PCR (polymerase chain reaction) is an amazing tool for use in clinical and diagnostic medicine and research, but there is more than just one kind, all with different applications and levels of sensitivity. This is a whirlwind trip around the subject, and isn’t exhaustive – please post any other techniques that you use in the comments.

  • AFLP PCR – involves the digestion of DNA into fragments using restriction enzymes, amplification of the fragments using PCR, and then analysis of the fragments using gel electrophoresis
  • Allele-specific PCR – this uses allele-specific primers that are designed to match a mutation
  • Alu PCR – uses primers that select the Alu elements (commonly repeated sections of DNA) and amplify the sections between these in DNA fingerprinting
  • Assembly PCR – also known as polymerase cycling assembly or PCA – uses PCR to build longer pieces of DNA from fragments using overlapping primers
  • Asymmetric PCR – amplifies just one strand of the target DNA
  • Colony PCR – used to screen colonies of bacteria after transformation with a plasmid
  • Conventional PCR – the basic PCR process, which produces up to a billion copies of a DNA or RNA strand; the results are only seen at the end of the process
  • Hot start PCR – inactivates the Taq polymerase until the reaction starts, using antibodies that are denatured by heat
  • In situ PCR – PCR that takes place in cells, or in fixed tissue on a slide
  • Inverse PCR – amplifies DNA next to a known sequence, using primers placed in the reverse direction to normal
  • ISSR PCR (intersequence-specific PCR) – amplifies DNA between sequences that are repeated through the genome
  • LATE PCR (linear after the exponential PCR) – creates single strands of DNA using PCR techniques
  • Long range PCR – uses a mixture of polymerases to amplify longer stretches of DNA
  • Methylation-specific PCR – uses two primer pairs that bind to methylated and unmethylated DNA
  • Multiplex PCR – uses a number of pairs of primers to allow analysis of a number of fragments in a single sample
  • Nested PCR – after an initial 30-35 cycles of PCR, an additional round of PCR uses new primers ‘nested’ within the original primers, making the process more sensitive because it reduces the risk of unwanted products from primers binding to incorrect regions
  • qPCR – in quantitative PCR (also known as real time PCR, RT PCR or qRT-PCR), the DNA or RNA molecules are tagged using fluorescent probes, so that the concentration of amplified products can be monitored and quantified in real-time by tracking the level of fluorescence
  • Repetitive sequence-based PCR – PCR using primers that are complementary to repeated non-coding sequences in the genome
  • Reverse transcriptase PCR – confusingly, also known as RT PCR – creates cDNA (complementary DNA) by reverse transcribing RNA to DNA using reverse transcriptase
  • Single cell PCR – exactly as it sounds – PCR on a single, isolated, lysed cell
  • TD PCR (touchdown PCR) – this begins with an annealing temperature higher than optimum and reduces it each cycle to the optimum or ‘touchdown’ temperature, and this can improve the outcomes

Suzanne Elvidge is a freelance science, biopharma, business and health writer with more than 20 years of experience. She is editor of Genome Engineering, a blog that monitors the latest developments in genome engineering and that aims to educate (and sometimes to entertain!) and has written for a range of online and print publications including FierceBiomarkers, FierceDrugDelivery, European Life Science, the Journal of Life Sciences (now the Burrill Report), In Vivo, Life Science Leader, Nature Biotechnology, PR Week and Start-Up. She specialises in writing on pharmaceuticals, biotechnology, healthcare, science, lifestyle and green living, but can write on any topic given enough tea and chocolate biscuits. She lives just beyond the neck end of nowhere in the Peak District with her second-hand bookseller husband and two second-hand cats.

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