A

Absolute Quantification:

Adapter:

A short chemically synthesized DNA double strand which can be used to link the ends of two DNA molecules.

Adenine (A):

One of the purine bases found in DNA and RNA (6-aminopurine), one member of the base pair A-T (adenine- thymine).

Alkaline Phosphatase:

An enzyme which catalyzes the hydrolysis of phosphomonoesters of the 5' nucleotides. Used to dephosphorylate (remove phosphate groups from) the 5' ends of DNA or RNA molecules, to facilitate 5' end-labeling with 32P added back by T4 polynucleotide kinase; or to dephosphorylate the 5' ends of DNA molecules to prevent unwanted ligation reactions during cloning.

Allele:

An allele is one of the alternative (two or more) forms of a particular gene inherited separately from each parent; usually found at the same locus on homologous chromosomes. Equivalent genes in the two sets might be different, for example because of single nucleotide polymorphisms.

Allele-Specific Ligation:

Technique permitting discrimination of two allele at locus by providing two short synthetic oligonucleotides that would bind adjacent to teach other on amplified DNA fragment, and would be ligated in presence of DNA ligase; if one of alleles containing mutation overlapped by 3'-end of one oligonucleotide, its ligation to oligonucleotide bound 3' to it would be prevented; to deduce identity of unknown allele, differentially labelled oligonucleotide pairs may be designed for each allele and their ligation efficiency compared in presence of unknown allele.

Allelic Discrimination Assay:

Assays designed to type for gene variants. Either differentially labeled (TaqMan®) probes (one for each variant) or a single probe and melting curve analysis can be used for this purpose. Alternative methods include dsDNA-binding dyes (in combination with melting curve analysis).

Allele-Specific PCR (AS-PCR):

Refers to amplification of specific alleles, or DNA sequence varients at same locus; specificity is achieved by designing one or both PCR primers so that they partially overlap site of sequence difference between amplified alleles.

Alternative Splicing: Refers to fact that certain genes retain or omit particular exons in the final spliced transcript.

Alu Sequence:

A family of sequence-related elements about 300 bp in length approximately 500 000 copies of which are scattered along the human genome.

Amber Codon:

It is the nucleotide triplet UAG one of the three codons that cause the termination of protein synthesis.

Amber Mutation:

It descibes any change in the DNA that creates an amber codon at a site previously occupied by a codon representing an amino acid in a protein.

Aminoacyl-tRNA:

It is the transfer RNA carrying an amino acid.

Amphipathic:

Structures that have two surfaces:one hydrophilic and one hydrophobic.

Amplicon:

The amplified sequence of DNA in the PCR process.

Amplification Plot:

The plot of cycle number versus fluorescence signal which correlates with the initial amount of target nucleic acid during the exponential phase of PCR.

Anchor & Reporter Probes:

Two partnering LightCycler (hybridizing) probes that hybridize on the target sequence in close proximity. The anchor probe (donor) emits fluorescence to excite the reporter probe (acceptor) to initiate FRET. In allelic discrimination assays, it is important that the reporter probe spans the mutation and has a lower Tm than the anchor probe.

Annealing:

It is the pairing of the complementary single strands of DNA to form a double helix.

Anticodon:

The 3-base sequence of a tRNA that base-pairs with the mRNA codon to effect translation of the mRNA into polypeptide sequence.

Anticoding Strand:

It is the strand of duplex DNA that is used as a template to direct the synthesis of RNA that is complementary to it.

Antigenic Variation:

Mechanism to ensure rapid sequence variation of the gene(s) encoding homologues of an individual protein antigen; usually involving multiple, related gene copies.

Antisense Construct:

Plasmid that contains coding region of gene placed adjacent to promoter in such orientation as to cause gene to be transcribed from DNA strand complementary to that from which RNA is normally transcribed.

AP-1 Site:

The binding site on DNA at which the transcription "factor" AP-1 binds, thereby altering the rate of transcription for the adjacent gene. AP-1 is actually a complex between c-fos protein and c-jun protein, or sometimes is just c-jun dimers. The AP-1 site consensus sequence is (C/G) TGACT(C/A) A. Also known as the TPA-response element (TRE). (TPA is a phorbol ester, tetradecanoyl phorbol acetate, which is a chemical tumor promoter).

Apoptosis:

It is the capacity of a cell to undergo programmed cell death.

Arrayed Library:

Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two-dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Arrayed libraries of clones can be used for many applications, including screening for a specific gene or genomic region of interest as well as for physical mapping.

ATG or AUG:

The codon for methionine; the translation initiation codon. Usually, protein translation can only start at a methionine codon (although this codon may be found elsewhere within the protein sequence as well). In eukaryotic DNA, the sequence is ATG; in RNA it is AUG. Usually, the first AUG in the mRNA is the point at which translation starts, and an open reading frame follows - i.e. the nucleotides taken three at a time will code for the amino acids of the protein, and a stop codon will be found only when the protein coding region is complete.

Autosomes:

All chromosomes except the sex chromosomes.

Autoradiography:

It detects radioactively labeled molecules by their effect in creating an image on photographic film.