Glossary of Terms for Molecular Technology

Active site The part of protein that must be maintained in a specific shape if the protein is to be functional.

Allele One of two copies of a gene.

Amino acid A peptide; the basic building block of proteins.

Amplicon Replicated target molecules created by polymerase chain reaction or other nucleic acid amplification methods.

Amplification Increasing the number of copies of a desired DNA segment. The amplified regions are called amplicons.

Aneuploid cell A cell having a chromosome number that differs from the normal chromosome number for the species by a small number of chromosomes.

Annealing Spontaneous alignment of two single DNA strands to form a double helix.

Antibody A protein molecule, produced by the immune system, that recognizes a particular substance and binds to it.

Anticodon A nucleotide triplet in a tRNA molecule that aligns with a particular codon in mRNA under the influence of the ribosome so that the amino acid carried by the tRNA is inserted in a growing protein chain.

Antiparallel A term used to describe the opposite orientations of the two strands of a DNA double helix; the 5’ end of one strand aligns with the 3’ end of the other strand.

Avidin A protein that specifically binds to biotin with usually high affinity.

Autoradiography The exposure of roentgenographic film to a blot or membrane containing a radiolabeled probe, used to locate the labeled probe

Bacteriophage A virus that infects bacteria

Base One nucleotide consisting of a nucleoside, pentose sugar and triphosphate; building blocks for either DNA or RNA

Base analog A chemical whose molecular structure mimics that of a DNA base; because of the mimicry, the analog may act as a mutagen.

Base pair (bp) One pair of complementary nucleotides (e.g. adenine to thymine or guanine to cytosine) on opposite sides of the duplex strands

Cell cycle The set of events that take place in the divisions of mitotic cells. The cell cycle oscillates between mitosis (M phase) and interphase. Interphase can be subdivided in order into G1, S phase and G2. DNA synthesis takes place during S phase. The length of the cell cycle is regulated through a special option in G1, in which G1 cells can enter a resting phase call G0

Chromosome Structure of DNA and associated proteins that contain the hereditary material within the cell. Genes are organized in linear arrangement in the chromosome.

Cistron Segments of DNA corresponding to one polypeptide chain, plus transcriptional start and stops signs.

Cloning The process of generating a large number of identical DNA fragments, typically to produce a probe for a specific gene.

Codominance The situation in which a heterozygote shows the phenotypic effects of both alleles.

Codon A sequence of three nucleotides that specifies a particular amino acid

Competent Able to take up exogenous DNA and thereby be transformed.

Complementarity The specific binding of adenine to thymidine (or uracil in RNA) and cytosine to guanine on opposite strands of DNA or RNA.

Complementary DNA or Copy DNA(cDNA) DNA generated form mRNA by the use of reverse transcriptase.

Complementary RNA Synthetic RNA produced by transcription from a specific DNA single-stranded template.

Complementation The production of a wild-type phenotype when two different mutations are combined in a diploid or a heterokaryon.

Cosmid A genetically engineered construct containing sites from lambda phage that allow for insertion of large pieces of DNA (30-50 kb). Recombinant cosmids can then be replicated in bacterial hosts.

Degenerate code A genetic code in which some amino acids may be encoded by more than one codon each.

Degradation Due to physical shearing or exposure to endogenous or exogenously added nucleases, DNA and RNA can become hydrolyzed or degraded to the oligonucleotide or single-nucleotide level.

Denaturation The process of making double-stranded DNA single stranded.

Dideoxy sequencing A method of DNA sequencing in which dideoxynucleotide triphosphates (ddNTPs) are used in the growing oligonucleotide chains synthesized from the DNA template, thereby terminating elongation.

DNA Deoxyribonucleic acid

DNAase Deoxyribonuclease, an endonuclease that randomly hydrolyzes (nicks) DNA at single sites on either strand of the DNA

DNA ligase An enzyme that covalently joins two pieces of double stranded DNA.

DNA polymerase The enzymes(s) that make DNA by the addition of bases to the end of the replicating DNA strand.Also has an editing function that can repair nicked DNA by removal of old nucleotides and replacement with new (e.g. labelled) nucleotides.

Dominant allele An allele that expresses its phenotypic effect even when heterozygous with a recessive allele; thus if A is a dominant over a, then A/A and A/a have the same phenotype.

Dominant phenotype The phenotype of a genotype containing the dominant allele; the parental phenotype that is expressed in a heterozygote.

Dot (slot) blot The immobilization of DNA or RNA to a sample spot (slot) on a filter that will be subsequently probed by hybridization. Usually many samples are applied, each to a different location on the same filter, for mass screening.

ds Double stranded

End-labeling The incorporation of nucleotides at the 5‘ end of a strand of DNA by the use of specific enzymes as one means of making labeled probes.

Endonuclease Enzyme that hydrolyzes dsDNA at internal locations

Enhancer A regulatory sequence that can elevate levels of transcription from an adjacent promoter. Many tissue-specific enhancers can determine patterns of gene expression in higher eukaryotes. Enhancers can act on promoters over many tens of kilobases of DNA and be 5’ or 3’ to the promoter that they regulate. Generally they are on the same chromosome.

Ethidium bromide A chemical dye that intercalates between the bases in DNA and causes DNA to fluoresce when illuminated with ultraviolet light.

Euploid A cell having any number of complete chromosome sets or an individual composed of such cells.

Exon The portion of a gene that is actually translated into protein. [Eukaryotic genes only.]

Exonuclease Enzyme that hydrolyzes ss or ds NA from the ends

Fingerprint The characteristic spot pattern produced by electrophoresis of the polypeptide fragments obtained through denaturation of a particular protein by a proteolytic enzyme.

FISH Fluorescent in situ hybridization. In situ (in the physical location) hybridization using a probe coupled to a fluorescent molecule.

Frame-shift mutation The insertion or deletion of a nucleotide pair or pairs, causing a disruption of the translational reading frame.

Functional genomics The study of patterns of gene expression and interaction in the genome as a whole.

Gene A sequence of nucleotides that code for a protein product.

Gene dose The number of copies of a particular gene present in the genome.

Gene locus The specific place on a chromosome where a gene is located.

Gene therapy The correction of a genetic deficiency in a cell by the addition of new DNA with or without its insertion into the genome.

Genetic code The set of correspondences between nucleotide pair triplets in DNA and amino acids in proteins.

Genetics The study of genes.

Genome The complete set of hereditary factors of an organism, contained in the chromosome.

Genomic library Collection of DNA fragments (library) whose sum represents the entire genomic DNA of an organism.

Genotype The specific genes that are present in an individual; they may or may not be expressed.

Germ line The cell lineage in a multi-tissued eukaryote from which the gametes derive.

Growth factor Signaling molecules, usually secreted polypeptides, that induce cell division in cells receiving theses signals. Signals can be autocrine (self derived), paracrine (from another cell but local in origin), endocrine (from a distant cell/organ) or neurocrine (from nerve cells).

Haploid A cell having one chromosome set or an organism composed of such cells.

Heteroduplex A DNA double helix formed by annealing single strands of a heteroduplex DNA.

Heterozygote An individual having a heterozygous gene pair.

Homology Similarity between two distinct genes in their nucleotide sequence.

Hybridization The process of complementary base pairing between two single strands of DNA, DNA and RNA, or sense and anti-sense RNA.

Inhibitor As it pertains to DNA manipulation in vitro, contamination in the preparation or sample can inhibit the biochemical processes involved in the manipulation, generally polymerases. Can be endogenous (from the sample matrix) or exogenous.

In situ hybridization Use of labeled DNA or RNA probes to localize complementary sequences within a cell.
Intron A portion of a gene not translated into protein, even though it is transcribed into RNA. A splicing event removes it from the primary RNA transcript leaving only the exons in the mRNA. [Eukaryotes only.]

Inverted repeat sequence A sequence found in identical form, but inverted. Commonly found in transposons and viruses.

Kilobase (kb) Unit of 1000 base pairs of DNA or 1000 bases of RNA.

Labeling The process of marking a DNA molecule using radioactive or non-radioactive labels.

Ligase An enzyme that can rejoin a broken phosphodiester bond in a nucleic acid.

Ligase chain reaction (LCR) An in vitro nucleic acid amplification method that uses DNA ligase, an enzyme that joins two pieces of DNA together.

Lagging strand In DNA replication, the strand that is synthesized apparently in the 3’ to 5’ direction, by ligating short fragments synthesized individually in the 5’ to 3’ direction. The short fragments called Okazaki fragments are primed using snRNAs.

Locus The site on the chromosome where a gene is located.

Missense mutation A mutation that alters a codon so that it encodes a different amino acid.
mtDNa Mitochondria DNA.

Mutation The process that produces a gene or a chromosomal set differing from the wild type.

Nick translation A means of incorporating labelled nucleotides into a segment of nucleic acid by displacing random nicks (introduced by DNAase) through the use of DNA polymerase.

Nonsense codon A codon for which no normal tRNA molecule exists; the presence of a nonsense codon causes termination of translation (ending of the polypeptide chain). The three nonsense codons are called amber, ocher, and opal.

Nonsense mutation A mutation that alters a gene so as to produce a nonsense codon.

Northern blot RNA immobilized on a solid support after separation according to size by electrophoresis.

Nucleotide (nt) The structural unit of nucleic acid consisting of phosphate, sugar and purine or pyrimidine base.

N-Terminus and C-Terminus The two ends of a protein/polypeptide chain. Protein sequences are given N?C in direction.

Oligonucleotide A short (10-100 nt) stretch of ssDNA usually prepared by a series of chemical reaction following a known sequence.

Oncogene A type of gene associated with cancer production.

Operon A set of adjacent structural genes (prokaryotic) whose mRNA is synthesized in one piece, plus the adjacent regulatory signals that affect transcription of the structural genes. Regulation can be postive (turn it on when needed) or negative (keep it off until needed).

ORF (open reading frame) A section of a sequenced piece of DNA that begins with a start codon and ends with a stop codon; it is presumed to be the coding sequence of a gene.

Phenotype The form or expression taken by some character or gene in a specific individual. Genotype is not always reflected in the phenotype.

Point mutation A mutation that can be mapped to one specific locus.

Polymerase chain reaction (PCR) Enzymatic technique to create multiple copies of one sequence of DNA

Plasmid A small, circular, extrachromosomal, self-replicating piece of DNA found in some bacteria (e.g. pBR322). Used in cloning (cloning plasmid = vector).

Poly(A)tail A string of adenine nucleotides added to mRNA after transcription.

Polycistronic mRNA An mRNA that encodes more than one protein (prokaryotes and viruses).

Polymorphism The occurrence in a population of several phenotypic forms associated with alleles of one gene or homologs of one chromosome

Primer A short single-stranded DNA or RNA that can act as a start site for 3’ chain growth when bound to a single-stranded template.

Probe A fragment or sequence of ssDNA, dsDNA or RNA that will be hybridized to a complementary sequence of nucleotides in another single-strand nucleic acid (target). Probes are labeled in some what to make the reaction visible.

Promoter A regulator region a short distance from the 5’ end (transcription start site) of a gene that acts as the binding site for RNA polymerase.

Reading frame The codon sequence that is determined by reading nucleotides in groups of three from some specific start codon.

Recombinant DNA The DNA molecule produced from inserting DNA from one organism into another piece of DNA by using genetic engineering techniques.

Regulatory genes Genes that have roles in turning on or off the transcription of other genes.

Replication The process of making DNA.

Replication fork The point at which the two strands of DNA are separated to allow replication of each strand.

Restriction enzyme Another name for restriction endonuclease.

Reverse Transcriptase An enzyme capable of synthesizing ssDNA from RNA. From retroviruses.

Ribosomal RNA (rRNA) A class of RNA molecules that have an integral role in ribosome structure and function.

RNA Ribonucleic acid, the single stranded nucleic acid of three types; mRNA (messenger RNA), tRNA (transfer RNA) and rRNA (ribosomal RNA)

RNA polymerase A DNA directed RNA polymerase that creates a strand of RNA complementary to one strand of the dsDNA template.

RNases Ubiquitous enzymes that degrade RNA

Sequencing A method that determines the actual sequence of the nucleotide bases in DNA or protein.

Signal sequence The N-terminal sequence of a secreted protein, which is required for transport through the cell membrane.

Southern blot DNA that has been separated by gel electrophoresis, transferred from the gel to an immobile support (e.g. nitrocellulose or nylon), and bonded onto the support in single-stranded form ready for hybridization
ss Single stranded

Staggered cuts The cleavage of two opposite strands of duplex DNA at points near one another.

Streptavidin A bacterial form of avidin that has a slightly stronger affinity for biotin than does avidin form egg white.

Stringency The conditions of hybridization that increase the base-pairing of binding between two single strand portions of nucleic acid.

Supercoil A closed, double-stranded DNA molecule that is twisted on itself.

Target nucleic acid DNA or RNA to be hybridized with the labelled probe.

Tissue-specific gene expression The expression of a gene in a specific and reproducible subset of tissues and cells during the development of a higher eukaryote.

Transcription The process of producing an RNA copy from a DNA template.

Translation The production of protein from messenger RNA.

Uracil-N-glycosylase An enzyme that digests DNA that was replicated using dUTP instead of dTTP and is used to prevent amplicon carry over contamination.

Vector A plasmid, bacteriophage, cosmid or virus that carries foreign DNA into a host organism.

Western blot Proteins that have been separated by acrylamid electrophoresis, transferred and immobilized onto a solid support, then probed with labelled antibody.

Dr. Rachel Boulay Assistant Professor & Director of Education
John A. Burns School of Medicine University of Hawai’i at Manoa
651 Ilalo Street | Biosciences Building 311f | Honolulu, HI 96813 | Ph: (808) 692-0986 | Fax:(808) 692-1973