Multi-well Filter Plate Glossary of Terms
ADENINE A purine base that is one of the building blocks of DNA. Adenine binds with thymine in DNA and with uracil in RNA.
ADMET An acronym for Adsorption, Distribution, Metabolism, Excretion and Toxicology.
AFFINITY A measure of the binding strength between two molecules. An example is that streptavidin has a high affinity for biotin.
AGAROSE A polymer that is used as a matrix for electrophoresis.
AMINO GROUP The –NH2 group. Amino groups are weakly basic and are found in organic molecules. Important for biochemists in order to bind and sequence peptides.
AMINO TERMINUS The N-terminus region of a polypeptide. The amino terminus end of a polypeptide contains the free amino group.
AMPHOTERIC Reacts as either an acid or a base. In the presence of an acid, amphoteric molecules react as bases. In the presence of bases, they react as acids.
ANALOG A molecule that is either functionally or structurally related to another molecule.
ANION A negatively charged ion.
ANTIBODIES Antibodies are proteins (immunoglobulins) synthesized by the immune system in response to an antigen. They are Y-shaped, with a “tail” and two “arms”. The arms have a unique shape that enables them to combine specifically with the antigen. This plays an important role in the body’s defense against infection (bacteria, viruses) or other foreign protein substances. The specificity of the antibody-antigen reaction forms the basis for highly specific and sensitive immunoassays. They can be used to purify specific molecules from a mixed solution using affinity.
ANTIGEN A substance capable of stimulating the production of antibodies in living organisms and reacting specifically with them.
APTAMERS Short strands of DNA that bind protein targets.
ASSAY A method/procedure for detecting the presence, estimating the concentration, and determining the biological activity of a macromolecule, molecule, ion, or cell. Features of an assay include: sensitivity, the ability to detect small amounts of a substance or molecule and specificity, the ability to detect only the analyte. Assays employ measurable parameters that allow for the evaluation of differences between samples and controls.
AUTORADIOGRAPHY A method for detecting radiolabeled molecules using X-ray film. It is typically done after gel electrophoresis.
BACKGROUND Effects that obscure a specific signal such as background “noise” in chart recorders. In transfer membranes, background results from probes attaching to sites other than the specific or complementary molecules. Blocking the nonspecific sites with substances to which the probe will not bind can prevent this.
BASE PAIR A unit of measure to determine the length of a nucleic acid.
BIOMARKER A molecular marker that is associated with or identifies biological function.
BIOTINYLATED Labeled with biotin. Biotinylated probes are used in assays based on the strong affinity that the glycoprotein avidin (or streptavidin) has for biotin. Chromogenic, fluorogenic, or enzyme conjugates of avidin are used in such assays. Biotinylation is the covalent linkage of biotin to DNA and proteins.
BLOCKING The act of preventing unwanted molecules from binding to a surface. It is commonly used to prevent antibodies or DNA from binding directly to a membrane instead of binding to a desired biomolecule. It is often done by adding milk proteins (casein) to a protein blot or salmon sperm DNA to a nucleic acid blot after the target molecules have been attached.
CARBOXYL GROUP The –COOH functional group found in organic molecules. Carboxyl groups are acidic in nature.
CARBOXYL TERMINUS The end of a polypeptide that contains the free carboxyl group.
CATION A positively charged ion.
CCD CAMERA A camera that uses charged couple device (CCD) chips to convert photons to electrical or digital images. It is used in many microarray scanners.
cDNA Complementary DNA. cDNA is a single stranded piece of DNA that is complementary to a piece of RNA.
cDNA LIBRARY A collection of cloned DNA molecules that are complementary to the entire set of mRNA molecules obtained from a cell, organism, or tissue.
CHAOTROPIC AGENT An ion that solubilizes proteins, dissolves cell membranes, and denatures DNA.
CHELATE The complex formed between a metal ion and an organic liquid, which has more than one binding site. EDTA is a common chelating agent to remove Mg or other metal ions from availability in solution.
CHEMILUMINESCENCE The process by which an enzyme is able to catalyze a chemical reaction that results in the production of light. This is commonly used by attaching an enzyme to an antibody. This conjugate is then allowed to bind to a blotted protein mixture on a membrane that has been blocked. If it remains after the wash, it can be used to detect the specific protein to which the antibody has affinity. A subsequent step is needed to add chemicals that react with the conjugated enzyme to produce light that can be detected on X-ray film. It is also used to detect DNA hybridization by adding an antibody step to the detection process, while this works well in most cases; researchers prefer a direct label if possible.
CLINICAL TRIAL There are three phases to a human clinical trial. Clinical trials are designed to evaluate the effectiveness, both positive and negative, of a new drug in a human population.
COMBINATORIAL CHEMISTRY A method for assembling and manipulating molecular and chemical building blocks to create new compounds.
COMPOUND A casual name referring to a specific molecule.
CONTROL A standard, which is used to compare experimental results to (A.K.A. benchmark).
CPS Counts per second. When detecting the activity of a tag it can be measured by a scintillation counter (radioactivity) or a Multilabel counter for fluorescence. It relates to the number of photons detected by the radiation counter or fluorescence counter. The greater the counting efficiency, the closer the CPS values are to the actual number of photon produced.
CRO Contract Research Organization.
CROSSTALK An event where the sample from one well becomes contaminated with the sample(s) from adjacent wells. Crosstalk is also referred to as cross contamination.
CV Coefficient of Variation. A measure of the variation that can occur between samples during a binding assay. Variation can result from liquid transfer, non-specific binding, improper washing and anomalies with the plate.
CYTOKINE A type of protein that is released by cells. Cytokines control numerous cellular functions including cell growth, differentiation, and the inflammatory response.
CYTOKINE ASSAY An assay to measure the presence and amount of cytokine proteins. Cytokine assays are often performed to see if a particular drug is capable of effecting one or more cellular responses (cell growth, proliferation, differentiation, apoptosis, etc.) ELISPOT assays are one form of cytokine assay.
CYTOSINE A pyrimidine base that is found in DNA. Cytosine pairs with guanine in DNA.
DENATURE The loss or change of the native 3-dimensional structure of a biomolecule.
DETECTOR Name given to a device that performs some type of quantitation of a signal from a tagged molecule.
DNA POLYMERASE An enzyme molecule that catalyzes the synthesis of DNA into a sequence complementary to a DNA or RNA template.
DNA SEQUENCING Deciphering the order of bases within a piece of DNA.
DRUG CANDIDATE Name given to a molecule discovered in R&D that elicits a desired biologic response. After their discovery in R&D, drug candidates move down the drug discovery pipeline and are tested for ADMET properties and their ability to produce a desired biologic response in animal and human subjects.
DYE TERMINATOR Used in DNA sequencing. It is a fluorescently labeled dideoxy nucleotide, which is added to a DNA synthesis reaction. When it randomly incorporates into a growing DNA strand it terminates the synthesis at one of the four bases. This allows the determination of the sequence of the DNA when the samples are electrophoresed and detected.
ENZYME A protein that catalyzes a specific chemical reaction(s).
ELISA Enzyme-linked immunosorbent assay. ELISA relies on the specific interaction of an antibody with its matching target protein, referred to as antigen, to analyze complex protein samples. They may be used to detect either antibodies or antigens. ELISA assays come in many forms, such as indirect, sandwich and competitive.
ELISA (COMPETITIVE) Used to define antigenic specificity. Sample antibodies and enzyme-labeled antibodies compete for binding to an antigen or antigen-coated plate.
ELISA (INDIRECT) Used to screen for proteins. Sample antibodies (referred to as primary antibodies) bind to an antigen or antigen-coated plate. Another antibody (referred to as secondary antibody) is then added which binds to the first antibody and the amount of sample is detected by enzymatic detection.
ELISA (SANDWICH) Used to quantitate antigen. Sample antigen is bound to an antibody or antibody-coated plate. The amount of sample is detected by enzyme-labeled secondary antibodies.
ELISPOT A membrane-bottom plate ELISA assay where an antibody against a specific cytokine is bound to a membrane instead of a styrene plate. Then cells are added and if they produce the appropriate cytokine it will bind to the antibodies on the membrane. After washing away the cells, a second antibody against the cytokine is added that is labeled and will show a spot where the secreting cells lie. Often the membrane is punched out and analyzed under a microscope.
EMISSION The release of light at a different color (wavelength) indicating the presence of a specific fluorescent molecule (picoseconds after excitation). Time resolved emissions are longer (microseconds) allowing the background emission from other fluorescent molecule to decay prior to reading. This allows greater sensitivities.
ENZYME ASSAY An experiment in which enzymes are used to perform some sort of specific reaction.
Assays can include the determination of the rate of reaction (activity) as well as the specificity for a particular molecule.
EUROPILATED This refers to the attachment of Europium (Eu) as a tag for the detection of time-resolved fluorescence. Most Eu assays include the attachment of an Eu chelate to a ligand or antibody that is opened by a releasing agent after washing. This allows the Eu to be detected in solution.
EUROPIUM (Eu) A metal of the rare earth group that has a chemical property that allows it to be used for time resolved fluorescence (TRF). It can only be used as a tag by attaching a Europium chelate to a ligand or antibody. Typically Eu is detected in solution after release from the chelate.
EXCITATION Laser light of a specific color (wavelength) that is absorbed by certain types of molecules exciting them to a higher energy state. It is important that the stokes-shift be large enough that the excitation wavelength be far enough away from the emission wavelength to prevent interference.
EXPRESSION The transcription and translation of a gene.
FEMTOMOLE A femtomole is equal to one quadrillionth of a mole (10-15 ).
FILTRATE The portion of the sample that comes through the membrane.
FLUORESCENCE Light emitted from a fluorophore (fluorescent molecule) as a result of excitation. The excitation wavelength (color) is different that the emission wavelength. This difference is known as the stokes shift. The emitted light is detected in a specialize detector like the PerkinElmer Wallac Victor. Most fluorophores give a simple emission that is about 1 picosecond after excitation while time-resolved fluorescence emits after a microsecond. Fluorescence is best detected with either the black or natural filter plates.
FLUOROMETRIC PROCEDURE Analytical procedure based on the ability of an analyte to emit visible light when exposed to ultraviolet irradiation.
FLUORESCEIN A very common fluorescent molecule that excites and emits in the blue-green color range.
GEL ELECTROPHORESIS A method for separating nucleic acids or proteins based on size through a gel matrix. The movement through the matrix is induced by an electrical current that is applied to the gel, the separation results from the tunable resistance provided by the gel.
GENE A region of DNA that corresponds to a single protein or RNA molecule. Genes are responsible for discrete hereditary characteristics. Genes includes both the functional and nonfunctional units of DNA.
GENETIC CODE The code that specifies how a nucleic acid sequence is translated into an amino acid sequence.
GENETICS The area of biology that studies heredity and variation.
GENOME The totality of genetic information of an organism.
GENOMICS The study of the structure and function of genes for the whole organism. A lot of other ‘omics have been coined but all relate to the search for genes based on the search criteria. For example, metabaomics studies pursue genes that are regulated in responses to the metabolism.
GUANINE A purine base that comprises DNA molecules. Guanine pairs with cytosine in DNA.
HALF-LIFE The time it takes for half of the activity of a molecule to decay.
HETEROGENEOUS A mixture. It can refer to a solution that contains a complex mixture of molecules. In drug discovery, a heterogeneous assay is one that requires separation (usually by filtration) of one or more of its components (for example, removal of unbound label) prior to detection.
HIGH THROUGHPUT SCREENING The process of performing an assay for a collection of millions of different compound at one time. These assays can be heterogeneous or homogeneous; the ultimate goal is to find drug candidates (leads) from this large collection of randomly synthesized chemicals.
HOMOGENEOUS In drug discovery it refers to a high throughput-screening assay where all of the cells and detection components are added together and detected. This assay is more capable of miniaturization and does not require a filtration step.
HYBRIDIZATION The process where two complimentary nucleic acid sequences form a double helix during the annealing process.
IMMUNOASSAY A sensitive analytical procedure using a highly specific antigen-antibody reaction and principles such as fluorescence, radioactivity, or enzymatic activity to measure biochemical substances which are either the antigen or the antibody in that reaction.
IMMUNODIAGNOSTICS The use of antibodies to detect genetic markers linked to diseases. Recently gene microarrays and protein arrays are being used to test the expression of a whole collection of genes at the same time.
IMMUNOGLOBULIN An antibody molecule. There are five types of immunoglobulins; IgG, IgA, IgE, IgD, and IgM. Each immunoglobulin molecule plays a specific role in the immune response.
IN SITU HYBRIDIZATION A method where single stranded DNA or RNA probes are used to locate a gene or mRNA molecule within a cell or tissue. Unlike standard hybridization procedures, in situ hybridization allows one to pinpoint the location of the gene or mRNA of interest.
IN VITRO In the test tube or in the laboratory. When used in a molecular context, in vitro refers to cells growing in culture as opposed to in an organism. When cells grow within an organism it is referred to as in vivo. An in vitro assay is one that is performed in a test tube in a lab as opposed to inside an organism.
ION An atom with either a positive or negative charge.
ISOELECTRIC FOCUSING The first dimension of 2-D electrophoresis. IEF is the movement of proteins through a stable pH gradient with the use of ampholytes.
ISOELECTRIC POINT The pH of a solution in which a protein has no net charge. At the protein’s isoelectric point, it will not migrate in the presence of an electric field.
ISOTOPE A form of an atom. Isotopes can be either stable or radioactive.
Kd / DISSOCIATION CONSTANT It is the concentration of a molecule (ligand) that is needed to saturate the binding of half of the available binding sites on the receptors. This is an important value because it is in the center of the region of linear response. Any changes to binding can be reliably assayed if you start at the Kd concentration.
KILOBASE 1,000 bases of DNA or RNA.
KINASE ASSAY An enzyme assay that detects the activity of an enzyme that can add phosphate groups to other molecules. It has been demonstrated that kinase activity is important for signal transduction and controlling gene expression, making them good targets for the development of drug leads.
LABEL/LABELED A label is a molecule that can be attached to another molecule. It has some property such as radioactivity, fluorescence, or luminescence to allow it to be detected along with the molecule to which it was attached. A molecule containing a label attachment is called tagged or labeled.
LEAD A molecule that exhibits the desired effect. The effect can be a therapeutic response or modulation of a specific molecular target.
LEAD DISCOVERY The R&D activities that result in the generation of leads, such as high throughput screening, microarrays, in vitro assays and expression studies.
LEAD OPTIMIZATION Physical alteration of the structure of the “lead” to produce more desirable ADMET properties or increased activity.
LIBRARY In drug discovery, it refers to a collection of molecules. When the molecules are small-synthesized compounds, the collection is called a combinatorial chemistry library. Other examples are DNA libraries and antibody libraries. An expression library is a collection of bacterial cells or phage, each containing a unique recombinant DNA construct created from a digested chromosome, cDNA (from RNA) and protein.
LIGAND A molecule or ion that can form a complex with another molecule, usually a macromolecule. Also, an organic molecule capable of forming coordinate covalent bonds with metallic ions. Can be natural or synthetic in origin.
LIPID An oil-soluble molecule. An example of a lipid is a fatty acid.
LUMINESCENCE The emission and detection of light produced by chemical reactions or bioluminescence due directly to the enzyme light production. These enzymes can be used as labels to trace a molecule of interest. It does not require laser excitation like fluorescence since it is a result of a chemical reaction. The use of white plates enhances the recovery of photons.
LYSIS The rupture of a cell membrane which releases the cytoplasm and ultimately leads to the death of the cell.
LYSATE The generally viscous and complex sample from the breakup of cells. Filtration often fouls without prefiltration.
MACROMOLECULE A large biomolecule such as a protein, nucleic acid or polysaccharide.
MALDI-TOF An acronym for maxtrix assisted laser desorption/ionization time of flight. MALDI-TOF is a mass spectrometry technique used for analyzing protein sequences.
MASS SPECTROMETRY A method for identifying molecules based on their mass-to-charge ratio of the ions generated from the molecule by vaporization and electron bombardment.
MESSENGER RNA mRNA. The RNA template used for protein synthesis.
MICRON Unit of measure equal to 10-6 meter.
MOLECULAR WEIGHT The relative molecular mass of a molecule. Molecular weight is typically expressed in Daltons.
MONOCLONAL ANTIBODY Immumochemically identical antibodies produced by a clone of plasma cells. Monoclonal antibodies are now being produced commercially using hybridomas.
nM Nanomolar, 0.000000001 Molar, a very dilute sample or perhaps only a few thousand molecules per mL of solution.
NORTHERN BLOT The method for separating RNA fragments via electrophoresis and then immobilizing them on a membrane support.
NUCLEIC ACID A chain of nucleotides joined by phosphodiester bonds. Nucleic acids can be either DNA or RNA.
OLIGONUCLEOTIDE A small chain of nucleic acids.
PCR Acronym for Polymerase Chain Reaction. The method of amplifying specific regions of DNA by multiple cycles of DNA polymerization. Each cycle of polymerization is followed by a brief heat treatment to separate complementary strands.
PEPTIDE A protein fragment or at least two amino acids joined by a peptide bond.
PHOTON A particle of light. Measure in ‘quanta’ of light needed to initiate an electron movement in a detector.
PLAQUE A clear zone around a layer of cells that is the result of an agent that lyses the cells.
PLAQUE LIFT A method of immobilizing proteins expressed from cones that are growing on an agar plate. Plaque lifts are done by using a piece of membrane to immobilize the plaques.
PLASMID Small circular DNA molecules that replicate independently of the genome. Plasmids are often used as vectors for DNA cloning.
POLYACRLAMIDE GEL A matrix of acrylamide polymers used for the separation of proteins and nucleic acids.
PAGE Polyacrylamide gel electrophoresis. The process of separating nucleic acids or proteins via electrophoresis.
POLYPROPYLENE A polymeric material which can be melted and which is resistant to a broad range of chemicals. It is generally low in biomolecule binding and therefore a good choice for 96-well plate construction.
POLYSTRENE A polymer commonly used in the production of 96-well plates as well as a number of laboratory devices. It can be treated so that it will tend to bind to cells allowing the culturing and washing of cells in plates that do not contain membranes. It is generally high in biomolecule binding and is not a good choice for binding assays because of the potential for high non-specific binding (background).
PREHYBRIDIZATION Blocking of unoccupied sites of a DNA blot by unlabeled DNA of another species. This ensures that as many sites are occupied as possible to prevent non-specific binding and high background levels. Salmon sperm DNA, fragmented by sonication, is often used to prehybridize membranes. Recently many labs have done away with prehybridization steps, sometimes it works sometimes the prehyb is needed.
PRIMER Oligonucleotides that can be extended by DNA polymerase.
PROBES Labeled substances, which have specific affinity for the transferred proteins, DNA or RNA. Radioactive, chromogenic, fluorogenic, or enzyme conjugates of antibodies, lectins or protein A and complementary DNA’s or RNA’s are among the probes used (see tags and labels).
PROTEASE-INHIBITOR ASSAY An enzymatic assay for the presence of protease inhibitors.
PROTEIN Made up of amino acids linked together in long chains. The individual chains are called polypeptides. At intervals along their lengths the individual polypeptide subunits are linked together via hydrogen and other types of weak bonds to make up protein. Proteins are synthesized in a process called translation and are extremely variable in structure. They are often described in terms of their size in kilodaltons Kd.
PROTEOMICS The study of protein synthesis and expression for the whole organism or proteome. Related to genomics but more complex since while there are about 50,000 gene sequences there are over 300,000 known proteins. Highly parallel purification schemes for proteins include multi-well filtration with ultrafiltration membranes.
PURINE A nitrogen containing ring compound that is found in DNA and RNA. Examples of purines are adenine and guanine.
PYRIMIDINE A nitrogen containing ring compound that is found in DNA and RNA. Examples of pyrimidines are thymine, cytosine, and uracil.
RECEIVER PLATE Solid bottom plate used underneath the filter plate to capture the sample that comes through the membrane for further processing.
RECEPTOR A molecule that sits on the cell surface/plasma membrane and binds to a ligand. Receptor-ligand binding assays are popular in high throughput screening.
RECOMBINANT DNA A DNA molecule formed by joining two different DNA segments from different sources.
RETENTATE The portion of the sample that is collected on top surface of the membrane.
SCINTILLATION COUNT Describes the process by which radioactivity is detected. Since radioactivity alone is difficult to measure, a radioactive sample is added to a cocktail containing a chemical that gives off light after it has been exposed to radiation. This amount of light is emitted is proportional to the amount of radiation present in the sample. A device called a Scintillation counter contains a very sensitive light detector and can approximate the radiation present in a sample to a high degree of accuracy.
SIGNAL-TO-NOISE RATIO The ratio of signal-to-background level. The higher its value the greater the confidence in the accuracy of the experimental results.
SINGLE NUCLEOTIDE POLYMORPHISM Single base pair variations or mutations between the DNA of a population. SNP’s can be scattered randomly throughout an organism’s DNA.
SMALL MOLECULES Generally refers to molecules that are smaller than proteins. In drug discovery they are often used as the backbone for the attachment of random groups forming a library of compounds, which are subsequently used to detect the binding of the small molecule construct to a target molecule.
SOUTHERN BLOT A method in which DNA fragments are separated via electrophoresis and then immobilized on a membrane for further analysis.
STOKES SHIFT The amount of difference between the excitation and emission color wavelengths given off by a fluorophore. The greater the difference, the less likely that the excitation light will interfere with the detection of the emission color (wavelength).
STREPTAVIDIN The binding partner to biotin (see biotin).
SUBSTRATE A substance on which an enzyme acts. See “Enzyme”. If you are ‘substrate limiting’ then the conversion of substrate to product is being done at maximum speed. If you are ‘enzyme limiting’ then your reaction speed will be a product of the concentration of enzyme.
TAG The addition of a molecule (label) to another to allow it to be detected. Common tags include radioactivity, fluorophores and enzymes.
TARGET The molecule chosen based on the possibility that modulation of this molecule may elicit a desired pharmacological response.
TARGET SELECTION The process by which it is determined which target is a good candidate for a choice for use when screening a library. The choice of targets often results from previous disease studies but currently some targets are being selected based on their similarity to gene sequences of known targets.
THYMINE A pyrimidine base found in DNA. Thymine pairs with adenine.
TIME RESOLVED FLUORESCENCE (TRF) A sensitive detection system patented by PerkinElmer Wallac. It uses lanthanide chelates that give an intense and long-lived fluorescence emission (>1000 microseconds), making it possible to measure fluorescence emission significantly later than excitation. This eliminates the background counts from short-lived fluorescence emitting from organic fluorophores that accompany the sample since they will have decayed prior to detection. This time delayed fluorescence in combination with a large stokes shift (340-615 nm) effectively reduces background emissions to a level that allows measurement sensitivity to rival and possibly exceed sensitivities achieved using expensive and dangerous radioactive tags.
TOXICITY STANDARDS Tests to indicate adverse reactions or lethality to drugs or drug components. Also used to assess biosafety of filters. Tests include appropriate combinations of direct injection, extraction and implantation. Generally known as USP Class I-VI Plastics tests.
URACIL A pyrimidine base found in RNA. Uracil pairs with adenine in RNA.
VACUUM The depression of pressure below atmospheric pressure. The maximum vacuum possible is about 30 inches of Mercury (Hg).
WEEPING The dripping of solution from the well of a multi-well plate through the bottom holes in the absence of centrifugation or vacuum filtration.
WESTERN BLOT Technique in which proteins are separated via electrophoresis and then immobilized on a membrane for further analysis.
WETTING AGENT A surfactant added to a membrane to assure complete intrusion (wetting) by a high surface tension fluid such as water. PVDF requires the addition of ethanol or methanol to prewet, and then water or buffer is rinsed through to remove alcohol residuals.
