This gel separates proteins on a two-dimensional sheet of gel, first in one direction based on the isoelectric point, then in the other direction based on the molecular weight of the proteins under investigation.
Building block of proteins; around 20 amino acids are present in proteins: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine.
Antibody
An inducible immunoglobulin protein that is produced by the B lymphocytes of the immune system. It recognizes and binds to a specific antigen molecule of a foreign substance introduced into the organism. Upon binding to corresponding antigens, the antibodies set in motion a process to eliminate the antigens.
Antigen
Any foreign substance (self - non-self discrimination), such as virus, bacterium, or protein. After introduction into an organism, the antigenic substances elicit an immune response by stimulating the production of specific antibodies.
Aptamer
DNA or RNA molecule which has been artificially manipulated to allow binding with other molecules and viruses.
Array technology
In a broader context, array technology refers to computer science, engineering and also telecomminications. The technology may involve 2D gel electrophoresis, CCDs, detection technologies, fiber optics, imaging, ink jetting, mass spectrometry, photolithography, phosphorimagers, piezoelectric, semiconductors and spotting robots.
Arrayer
Robot for making microarrays. The robot transfers clones from microwell plates to microscope slides.
BioChip
Miniaturised substrates onto which a large number of biomolecules are attached with high density and in a defined microarray.
Bioinformatics
Science dealing with the classification, storage, retrieval and analysis of genomic and proteomic information; molecular modelling.
Biosensor
Device in which recognition systems of biological chemicals are coupled to microelectronics to allow the low-level detection of substances such as proteins etc. in body fluids or pollutants in water.
Biotinylation
DNA probes are labelled with biotin. Biotinylated triphosphates are incorporated into the molecule by enzyme-dependent labelling reactions such as e.g. nick translation or random primed labelling. Afterwards, the probe is hybridised to the target. The location of biotin is visualised by complexing it with a streptavidin molecule that is attached to a colour-generating agent.
cDNA
Complementary DNA; DNA which is synthesised from a messenger RNA template which is complementary to the coding strand of genomic DNA.
cDNA arrays
Developed at Stanford University; the microarrays are glass slides on which cDNA has been deposited by high-speed robotic printing and suited for expression analysis of up to 10,000 cDNA clones per array from EST sequencing projects. The microarray measurements are carried out as differential hybridisations, namely mRNA from two different sources is labelled with two different fluorescent dyes, then passed over the array at the same time. The fluorescence signal from each mRNA population is evaluated independently to calculate the treated or control expression ratio.
Cell array
High-throughput characterisation of gene function using cell arrays.
High-density ordered array involving either living cells (microwells) or printed microarrays (slides). The latter involve full-length open reading frames of the genes in expression vectors that are printed at high density on a slide along with a transfection reagent. The slide is then placed in a cell culture plate and the microarray of DNA constructs is covered with adherent cells. Cells grow on top of the DNA spots, are transfected, and drive the expression of specific proteins.
DNA
Deoxyribonucleic acid consists of a polysugar-phosphate backbone from which the purines and pyrimidines project. The backbone is formed by bonds between the phosphate molecule and carbon 3 and 5 of the adjacent deoxyribose molecules. The nitrogenous base extends from carbon 1 of each sugar. It forms a double helix hold together by hydrogen bonds between specific pairs of bases (Watson-Crick model) and each strand in the double helix is complementary to its partner with regard to its base sequence.
DNA array
DNA arrays consist of large numbers of DNA molecules spotted in a systematic order on a solid substrate. Depending on the spotting technique used, the number of spots can range from hundreds to thousands.
DNA chip
These chips are also referred to as DNA arrays, or microarrays. Approx. 10,000 cDNAs can be spotted onto a microscope slide and subsequently be hybridised with a double-labelled probe.
DNA microarray
This kind of microarray consists of a set of regular arranged spots of DNA recognition elements (e.g. oligos) positioned on a rigid support. The diameters of the spots range between 20 and 200 micrometers. Usually 50 to 80,000 spots cover an area of approximately 1 square centimetre.
The technology is based on the selective recognition of gene sequences by hybridisation, namely the base-pairing of the 4 nucleotides. Upon hybridisation with e.g. a fluorescently-labelled sample (oligo, cDNA, mRNA, PCR product) the signals can be analysed.
Gene
Hereditary unit that occupies a specific locus within the genome or chromosome and which can have one or more specific effects on the phenotype of the organism. A gene can be present in various allelic forms.
Gene expression
The degree to which a gene is active in a certain tissue of the body, measured by the amount of mRNA in the tissue. General: transcription and translation of a gene into a protein recombinant.
Genetic marker
A piece of DNA or a gene whose properties (and sometimes also their position on the chromosomes) are known and can be used to identify particular cells or organisms; they might also be used as a reference point in a genetic mapping experiment.
Genome
The term describes the total genetic information of a specific unit of inheritance such as e.g., the nucleus or the mitochondria.
Genomic microarray
Technology that allows the assessment of multiple gene targets for the identification of gene amplifications or deletions in a different samples.
Genomics
The systematic and comprehensive analysis of the structure and function of the genome with the aim to identify and understand the role of genes.
HLA
Human leukocyte antigen; the HLA system is very complex and characterised by extreme polymorphism. There are many websites dealing with HLA or Mhc (Major histocompatiblity complex), among them http://syfpeithi.de where you will also find references to further interesting links to HLA.
HTS
High throughput screening
in vitro
Experiment performed in a test tube/laboratory apparatus
in vivo
in a living organism
Lab-on-the-chip
Microfabricated system for performing biochemical assays such as e.g. capillary electrophoresis, probe preparation, PCR reactions (microfluidics-based chips)
Manual spotting system
Microarrays can also be produced by manually spotting biomolecules onto glass slides. The total number of samples is however smaller than that spotted by an automated system. In addition, the pitch between adjacent features is greater than in an automated array (usual pitch 0.5 - 1.0 mm)
Marker
Marker can refer to
a gene with a known location on a chromosome and a clear-cut phenotype, that can be used as a point of reference when mapping a new mutant or antigenic markers that serve to distinguish cell types
Mass spectrometry
Technique uesed to measure and analyse a substance in terms of the ratios of mass to charge of its components.
Methylation
Methylation of cytosine (usually in CG stretches) --> sign for transcription factors to activate the gene and thus produce a protein. It is generally understood that genes that are available for transcription are sometimes less heavily methylated than the same genes in cells in which they are never expressed. It also refers to the addition of a methyl group to a chemical compound or macromolecule.
Microarray
Arrangement of miniaturised test sites on a small surface; spot sizes are usually less than 250µm. Many tests can be performed simulatenously or in parallel.
mRNA
messenger RNA; RNA molecule that functions during translation to specify the sequence of amino acids in a nascent polypeptide. In eukaryotes, mRNA is formed in the nucleus from premessenger RNA molecules.
Multiplex
This word is mainly used as 'multiplexing', thus referring to a method by which many parameters are simultaneously tested and processed.
Mutation
Change in the structure of DNA, thus leading to a change in the characterstics of an organism or indivudal cell as a result of altered protein or RNA content specified by the mutated DNA. One can differentiate for example between silent mutations, point mutations, back mutations, or somatic mutations.
Nucleotide
Monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose, and a phosphoric acid group. The nucleotides of DNA are deoxyadenylic acid, thymidylic acid, deoxyguanilic acid, and deoxycytidylic acid. Those of RNA are adenylic acid, uridylic acid, guanylic acid and cytidylic acid.
Oligonucleotide chips
Oligonucleotide chips consist of small glass plates with thousands of short 20-mer oligonucleotide probes attached to their surface. The oligos are synthesized directly onto the surface using a combination of semiconductor-based photolithography and light-directed chemical synthesis. Very large numbers can be probed; at present chips contain over 65,000 probes.
Peptide
Two or more amino acids are joined by a so-called peptide-bond.
Photolithography
Selective masking generates light patterns that direct chemical transformations to specific areas of photosensitive surfaces. Photolithography usually requires expensive equipment and particular knowledge; the technology is protected by patents
Piezoelectric
Becoming electrically polarised when subject to the mechanical stress; quartz for example produces an electric charge when squeezed.
Probe
In general, probe refers to any biochemical/nucleic acid/oligo etc. labelled with radioactive isotopes or tagged in other ways for identification. A probe is used to identify or isolate a gene, its product, or a protein. In microarrays, the probe is immobilised in regular arrangement on the substrate.
Protein arrays
Arrays consisting of proteins themselves or of probes used for capturing proteins.
Reader
Synonym for microarray scanner; after fluorescent labelling and hybridisation, the reader scans the microarrays into a computer for subsequent analysis.
Scanner
Also referred to as "reader"; after fluorescent labelling and hybridisation, the scanner or reader scans the microarrays into a computer for subsequent analysis.
SNP
Single nucleotide polymorphism; a site on the DNA strand at which the base sequence differs among individuals (Pronounce "snip").
SNP chips
Microarrays that are used for the genome wide genotyping of SNPs (single nucleotide polymorphisms)
Substrate
Substance on which an enzyme acts in biochemical reactions; or, in hybridisation arrays, the particular material onto which the biomolecules are deposited. These surfaces include glass, nylon, silicon or ceramic.
Target
Free nucleic acid sample/protein/etc. whose identity and abundance is to be detected.
