Real Time PCR - Some Basic Principles Glossary

amino acid

The basic building blocks of proteins. The sequence of amino acids in a protein and protein function are determined by the genetic code.

amplification

An increase in the number of copies of a specific DNA fragment.

antibody

Immune system protein made by mammals to specifically bind to foreign molecules allowing the mammal to fight off disease.

Bt corn

Corn that has been transformed with the Bt gene and is resistant to European corn borer.

Bt genes

Genes originating from the Bacillus thuringiensissoil bacteria that encode a protein toxic to the European corn borer.

chromosomes

The genetic structures in cells composed of condensed DNA ,which contain the genetic code for an organism.

coding region

Region of the DNA sequence between the promoter and the termination sequence. It contains the instructions about how to make a specific protein.

complementary

Term used in science to refer to the normal nucleotide-pairing in DNA replication, with cytosine pairing with guanine and adenine pairing with thymine.

denature

A process which breaks the H-bonds between DNA bases, making the molecule become single-stranded.

DNA

(deoxyribonucleic acid) The molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. It is the fundamental substance of which genes are composed.

DNA replication

The process in which a DNA molecule is copied. This takes place in PCR and naturally in cell division.

DNA sequence

The order of nucleotides, whether in a fragment of DNA, a gene, a chromosome, or an entire genome.

DNA template

That particular portion of a DNA molecule which is copied in PCR.

electrophoresis

A technique which uses electricity to separate molecule fragments according to size so they can be studied.

endogenous

Found naturally in an organism.

enzyme

A protein that catalyzes, or speeds up, a specific biochemical reaction without changing the nature of the reaction.

EPSPS

An enzyme that catalyzes a reaction in plant and bacteria cells that is necessary for the synthesis of some amino acids. Roundup herbicide binds to this enzyme preventing the production of amino acids and eventually starving the plant to death.

ethidium bromide

Dye molecule with a structure that binds to DNA and will fluoresce under ultraviolet light.

European corn borer

Ostrinia nubilalis (Hübner) is a major insect pest in corn that costs farmers millions of dollars annually in control expenditures and yield loss. The European corn borer (ECB) larva feed on the leaves and bore holes into the stalks where they tunnel.

event

The insertion of a particular transgene into a specific location on a chromosome. Events are differentiated by two factors: 1) what transgene was inserted, and 2) where on the chromosome it inserted and how many gene copies inserted at that locus.

flanking

In molecular biology, refers to two oligonucleotide being located adjacent to each other.

fluorescein

A fluorescent dye.

fluorescence

Light emitted by an excited singlet molecule as part of the de-excitation process. Because a small amount of the energy in the original exciting photon is lost by molecular vibration before the emission of the fluorescence, the wavelength of fluorescence is greater (i.e. less energy) than the wavelength of the exciting photon.

fluorophore

A molecule which fluoresces, give off light energy, when excited by an external light source.

FRET

Fluorescence Resonance Energy Transfer - a real time PCR DNA detection system, using flanking primers.

genes

The fundamental unit of heredity that carries genetic information from one generation to the next. A gene is an ordered sequence of nucleotides located on a particular position on a particular chromosome that encodes a specific functional protein.

genetic engineering

The process of adding foreign DNA to the genome of an organism.

genome

All the genetic material in the haploid set of chromosomes for a particular organism.

germplasm

The total of the inherited materials, or genes, in a species.

glyphosate

A herbicide which inhibits the production of amino acids.

hydrolysis

The reaction of a substance with water.

intercalating dye

A dye molecule which can insert between bases of DNA. Used in laboratories to detect DNA sequences.

intercalation

When a molecule, such as Ethidium Bromide or SYBR Green inserts in between DNA nucleotides of a double-stranded DNA moledule. Ethidium Bromide and SYBR Green are therefore, used in detecting the presence of DNA.

Lateral Flow Strip

A variation on the ELISA tests, using strips as opposed to microtiter wells to detect the presence of a protein produced.

nucleotide

A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule. Thousands of nucleotides are linked together to form a DNA strand.

oligonucleotides

Small fragments of nucleotides hooked together; primers used in PCR.

PCR

(polymerase chain reaction) A method for replicating a particular sequence of DNA in vitro. Used to generate greater amounts of DNA for analysis or to determine if a particular sequence exists.

phenotypes

The observable physical characteristics of an organism that are determined by a combination of the genetic composition (genotype) and the environment of the individual.

primers-dimers

Primer-dimers occur when single-stranded primer oligonucleotides bind to each other rather than the DNA template.

probe

A macromolecule such as DNA or RNA that has been labeled with either radioactivity or antibodies and can be detected by an assay. Probes are used to identify target molecules, genes, or gene products.

promoter

A specific DNA sequence to which RNA polymerase binds and initiates transcription. This region contains information which regulates when and how often the gene is transcribed and ultimately the amount of protein it produces.

protein

A large molecule composed of one or more chains of amino acids in a specific order. Proteins are necessary for the structure, function, and regulation of an organism's cells, tissues, and organs. Each protein has a unique function determined by its shape.

proteins

Large molecules composed of one or more chains of amino acids in a specific order. Proteins are necessary for the structure, function, and regulation of the organism's cells, tissues, and organs. Each protein has a unique function determined by its shape.

replicated

Copied DNA. To make copies of DNA.

resistance

The ability of an organism to survive and thrive in the presence of something that would normally cause damage or death, i.e., herbicide-resistant corn, Roundup-ready corn.

resistant

The inherited ability of a plant to survive and reproduce following exposure to a dose of herbicide normally lethal to the wild type. In a plant, resistance may be naturally occurring or induced by such techniques as genetic engineering or selection of variants produced by tissue culture or mutagenesis.

RNA

Ribonucleic Acid.  A single-stranded nucleic acid similar to DNA but having a uracil rather than thymine as one of the nucleotides. The RNA strand carries the coded information from the nucleus to the cytoplasm where protein production occurs.

Roundup

A herbicide that provides non-selective control of several annual and perennial weeds. Roundup will also damage crops, such as corn and soybeans that are not Roundup-resistant.

Roundup-Ready

A trade name given to certain varieties of corn or soybean which are resistant to the herbicide, Roundup, whose active ingredient is glyphosate.

RT-PCR

Real-time PCR.  This is a term used to describe PCR methods which detect DNA amplification in "real time" as the experiment is taking place, rather than at the end of the experiment.

susceptible

The inability to survive a herbicide at its use rate.

Taqman

A real time PCR probe detection system, using two labelled probes.

target DNA

The particular portion of the template DNA which is copied during PCR.

trait

The characteristic that results from an expressing gene(s). Ex. Upright leaves, drought tolerance, Bt resistance. A trait can be influenced by the environment.

transcription

The process by which the nucleotide sequence of DNA is copied into a single-stranded molecule of RNA. The nucleotide sequence of the RNA created is complementary to the DNA sequence except all thymine molecules are replaced with uracil molecules.

transgene

A gene that has been genetically altered. They are usually used to transform organisms.

transgenic

An organism that has a new genetically engineered DNA sequence found in every one of its cells. Genetically engineered organisms are transgenic. These two terms are used interchangeably.

variety

Crop plants within a species that have the same genetic composition. Because plants in a variety are usually heterozygous, their offspring will not remain genetically pure (i.e., corn hybrid varieties).

wavelength

The distance between equivalent positions in the electromagnetic wave formed by a photon as it moves through space. For visible photons, the wavelengths are in the range of 400 to 700 nm.