Glossary of Biotechnology Terms

Back to Array Experiments

• complementary DNA (cDNA): a DNA sequence which was produced from mRNA by reverse transcription. A cDNA is so-called because its sequence is the complement of the original mRNA sequence. However, when double-stranded cDNA is synthesized, it contains both the original sequence and its complement.
• cDNA library: a collection of cDNA's, each of which has been inserted in a DNA vector (e.g. a circular DNA plasmid) and replicated in a bacterium such as E. coli. The bacteria maintain a ready pool of the cDNA's and can be cultured to make copies of the library for many experiments. A population of bacteria containing a single inserted cDNA is called a clone. To extract a cDNA from the library, the insert from the corresponding clone can be amplified using PCR primed off the vector sequences connected to the ends of the cDNA.
• complement: The complement of a nucleic acid sequence replaces each base by its complementary base: adenine (A) by thymidine (T), cytosine (C) by guanine (G), and vice versa. In RNA, adenine is paired not with thymidine but with uracil (U). By convention, DNA and RNA molecules have a consistent orientation (5' to 3') which is used in writing their sequences. To preserve this orientation, the complement of a sequence is written backwards compared to the original. For example, an RNA sequence ACGGUACU has the DNA complement AGTACCGT.
• constitutively active: A constitutively active gene is always transcribed, regardless of any regulatory influences. Many, perhaps most genes are constitutively transcribed at some (possibly low) level; however, the level of transcription can be turned up or down by the action of regulatory genes.
• double-stranded: consisting of two bound strands, each of which is the complement of the other. DNA is usually double-stranded, while mRNA is not.
• emission wavelength: the wavelength of the light emitted by a fluorescent reporter molecule when stimulated by a laser at its characteristic excitation wavelength.
• excitation wavelength: the wavelength of the light required to stimulate emission by a fluorescent reporter molecule.
• expressed sequence tag (EST): a sequence from a transcribed mRNA for a possibly unknown gene. Individual EST's are neither especially informative nor highly accurate; however, they are easy to collect in large numbers. A database of EST's can be helpful for picking protein-coding sequences out of a long stretch of DNA, or for providing a larger context for very short sequences, such as the small pieces of protein sequence obtainable by mass spectrometry. EST's are compiled by the National Center for Biotechnology Information in a database called dbEST.
• gene transcription: the process by which a gene's DNA is read to produce messenger RNA.
• genetically heterogeneous: caused by more than one genetic factor that leads to the same phenotype. Many cancers, as well as other genetic diseases like type-I diabetes, are genetically heterogeneous. Note that this term is used when different genetic defects can independently cause disease. When multiple defective genes must combine to cause a disease, we say that they act in epistasis.
• genome: the collection of all genes in a cell. In a multicellular organism, every cell has a copy of the same genome, but not all cells express the same genes.
• hybridize: to bind complementary pairs of DNA molecules. A DNA molecule has a very strong preference for its sequence complement, so just mixing complementary sequences is enough to induce them to hybridize. Hybridization is temperature dependent, so DNA's that hybridize strongly at low temperature can be temporarily separated (denatured) by heating.
• mitosis: the process of cell replication by division.
• messenger RNA (mRNA): the type of RNA which codes for protein, as opposed to ribosomal RNA (rRNA) and transfer RNA (tRNA). mRNA is translated to protein by a cell's ribosomes.
• oligonucleotide: a short sequence (usually 2-50 bases) of DNA. Oligonucleotides of up to 30 bases are routinely synthesized from scratch for use as PCR primers or as probes for their sequence complements in a complex mixture of DNA.
• open reading frame (ORF): a DNA sequence which is believed, on the basis of statistical evidence, to code for protein, but for which no matching protein or mRNA is known. ORFs can often be confirmed by matching their sequences to a database of known genes or EST's.
• polymerase chain reaction (PCR): a technique for making many copies of a specific DNA sequence. The reaction is initiated using a pair of short primer sequences which match the ends of the sequence to be copied. Thereafter, each cycle of the reaction copies the sequence between the primers. Primers can bind to the copies as well as the original sequence, so the total number of copies increases exponentially with time.
• phenotype: the aggregate of all the observable characteristics of a cell or organism. The phenotype results from the expression of a subset of a cell's genome.
• polymerase: an enzyme which assembles nucleic acid residues into DNA or RNA polymers. Polymerases work from the DNA complement of the sequence to be built. DNA polymerases copy DNA to DNA to replicate the genome before mitosis, while RNA polymerases copy DNA to RNA as the first step in gene transcription.
• probe: in a microarray experiment, the solution of labeled DNA that is hybridized with the array. For comparative transcription studies, two cDNA probes are prepared from the total mRNA of two different kinds of cells and labeled with two different reporters.
• regulatory gene: a gene whose expressed product controls the transcription of other genes, either directly by DNA binding or indirectly by activating a cellular protein.
• reporter: a molecule which can be bound to cDNA and subsequently detected. Fluorescent reporters are used to detect the presence of cDNA on the spots of a microarray.
• reverse transcription: the copying of an RNA molecule back into its DNA complement. The enzymes that perform this function are called reverse transcriptases. Reverse transcription is is used naturally by retroviruses to insert themselves into an organism's genome. Artifically-induced reverse transcription is a useful technique for translating unstable mRNA molecules into stable cDNA.
• ribosome: a complex of protein and rRNA in the cytoplasm which can translate mRNA into protein.

Back to Array Experiments

URL: http://www.geneticengineering.org/jbuhler/glossary.html
Version: 0001. Last update: 26 June 2000.
Copyright 2000 by Jeremy Buhler (jbuhler@cs.washington.edu). All rights reserved.