Glossary

  Taq polymerase
A heat stable DNA polymerase isolated from Thermus aquaticus and used in PCR.
  annealing
The coming together of two complementary pieces of DNA to form dsDNA.
  annealing temperature
The temperature at which the primers in PCR bind to the complementary DNA prior to extension.
  cell lysate
The contents of cells which have been broken open.
  cloning
The transfer of a fragment of DNA of interest from one organism to a plasmid which can then be grown in a foreign organism and the DNA of interest amplified.
  cloning vector
Used in cloning to carry the foreign piece of DNA so that it can be transformed into bacteria and replicated. Commonly a virus or plasmid.
  codon usage
The bias shown by an organism for the particular codon which encodes an amino acid. The preferred codon for an amino acid may vary from species to species.
  degenerate primer
A primer with a choice of base in a particular position or positions allowing annealing and amplification of related sequences.
  denaturation
The disruption of the three-dimensional (tertiary) structure of a protein by heat treatment, pH or exposure to chemicals such as urea.
  elongation
A action which increases the length of a molecule or an object.
  exonuclease
An enzyme that cleaves nucleotide bases sequentially from the free ends of a nucleic acid (DNA or RNA).
  hairpin loop
A double-stranded region of single-stranded DNA or RNA formed by base-pairing between complementary base sequences on the same strand.
  homologous
Referring to genes with a high sequence identity. The similarity of sequences can be due to their common ancestry.
  Inosine
A nucleic acid base that fails to form specific bonds with another base (contrast with G:C or A:T) and thus can be used in a primer when there is uncertainty to the base found at a specified position.
  melting temperature
The temperature at which half the DNA strands are in a double helix and half are in a random state.
  mutagenesis
The process of changing the nucleic acid sequence of an organism.
  polymerase chain reaction
(PCR) A method to exponentially amplify a specific region of DNA in vitro using a heat stable enzyme and primers.
  polymorphism
The difference in DNA sequence of alternate alleles of a gene.
  primer
A pre-existing nucleic acid strand that serves as a starting point for DNA replication to which new nucleotides can be added.
  primer dimer
Two primers forming intermolecular bonds between complementary regions in preference to binding to the template DNA and thus reducing the yield of PCR product.
  quencher
A molecule which when it is in close proximity to a reporter molecule prevents it from giving off a detectable signal.
  reporter
A fluorescent molecule that gives off a signal. It can be used for detection and quantification of PCR product.
  restriction enzyme site
(restriction site) A specific sequence, often palindromic, that is recognised by a restriction enzyme and then cut in a defined way.
  site-directed mutagenesis
The changing of the nucleic acid sequence at a particular base and in such a way as to produce a selected change.
  thermal cycler
A machine containing a heating block that can be programmed to stay at a given temperature for a selected period of time. The programme can be repeated for the required number of cycles.
  thermostable
Referring to an enzyme which has the ability to remain intact and function at high temperatures e.g. Taq polymerase works at 72oC.
  touchdown
A form of PCR in which the initial annealing temperature is higher than that calculated. It is then lowered in stages over the following cycles allowing for increased specific binding.
© SCBC 2007