D-loop (displacement loop)
A structure formed when one strand of a duplex DNA molecule is displaced by a single-strand of homologous invading DNA. This reaction is catalyzed by the RecA protein in bacteria.

Defective phage
A phage that lacks one or more functions that are required for reproduction.

Defined medium
A bacterial growth medium in which all the components are known. Typically only includes the minimal growth requirements.

Deletion
The loss of one or more bases or base pairs from a molecule of DNA.

Deletion mapping
The use of deletion mutations to determine the position of overlapping point mutations for fine structure mapping of a genetic locus.

Denaturation of proteins
The unfolding of a protein molecule, usually by high temperatures or ionic detergents such as sodium dodecyl sulfate (SDS).

Denaturation of DNA or RNA
Separation of the two strands of a double-stranded DNA or RNA molecule by disrupting the hydrogen bonds that join the complementary bases from the two opposite strands, usually by heat or alkali. (Often called "melting".)

Density shift labeling
The addition of either a heavy or a light isotope to the growth medium which changes the density of the newly synthesized nucleic acids. For example, N14 is the natural isotope of nitrogen, so incorporation of N15 into DNA incr eases the density of the DNA.

Density-gradient centrifugation
Separation of molecules and particles on the basis of buoyant density, by centrifugation in a concentrated sucrose or caesium chloride solution.

Deoxyribonucleic acid
See DNA.

Derepression
The release of a gene or operon from repression so that it is expressed (or turned on).

Diauxic growth
A biphasic growth curve, typically resulting from the sequential use of multiple nutrients (e.g. glucose utilization followed by lactose utilization).

Dideoxynucleotide
A modified nucleotide that lacks the 3' hydroxyl group, preventing further chain elongation when incorporated into a growing polynucleotide.

Diploid
An organism which contains pairs of each chromosome.

Direct repeats
Two identical (or nearly identical) nucleotide sequences sometimes separated by a sequence of non-repeated DNA. For example,
3' TAGT . . . TAGT 5'
5' ATCA . . . ATCA 3'

Directed evolution
This term is used in two ways. (i) A laboratory process using mechanisms of natural selection to produce mutants adaptated to defined environmental challenges. This approach can be used to produce adaptions in single molecules, such as a RNA molecule or an enzyme. Since chemical reaction can occur very fast, multiple "generations" of molecules can be produced quickly. Microorganisms such as bacteria can also reproduce quickly, allowing multiple generations of selection in a short period of time. This approach has been used to produce novel enzymes with industrial and biomedical applications, and to produce bacteria with potential bioremediation applications. (i) The concept that under certain stressful conditions, there is a selection for those mutational changes that favor survival. This controversial concept, also called adaptive evolution, is essentially a molecular version of Lamarkian evolution.

Double-strand break (DSB)
A cut through both strands of the DNA backbone, resulting in two exposed double-stranded ends.

DNA (deoxyribonucleic acid)
A macromolecule usually made up of two antiparallel polynucleotide strands held together by weak hydrogen bonds and with deoxyribose as the component sugar.

DNA gyrase
A topoisomerase that removes supercoils from DNA by first producing double-strand breaks and then sealing them.

DNA ligase
The enzyme that joins the 5' and 3' ends of polynucleotide chains by the formation of a phosphodiester bond between them.

D-loop (displacement loop)
The structure formed when ssDNA pairs with a dsDNA molecule, disrupting the pairing of the original duplex DNA to form a hybrid between the ssDNA and one of the strands of the duplex DNA, and displacing the other strand from the duplex.

DNA polymerases
Enzymes that polymerize deoxyribonucleotides onto an existing polynucleotide chain using the complementary strand of DNA as a template.

DNA primase
The enzyme that normally synthesizes the RNA primers required for initiating DNA synthesis.

DNA Repair
A variety of different mechanisms that remove or modify damaged DNA.

DNase
An enzyme that degrades DNA.

dNTP
Deoxynucleotide triphosphates used in the synthesis of DNA -- deoxy-ATP, deoxy-TTP, deoxy-GTP, or deoxy-CTP.

Domain
A discrete, independantly folded region of a protein. Different functions of a multifunctional protein are usually localized in separate domains.

Dominant
The phenotype that is observed when two alleles of a gene are present in a cell. The gene whose phenotype is expressed is the dominant allele and the allele whose phenotype is masked is the recessive allele. If the phenotype of the diploid is inte rmediate between that of the two haploid genes, then the alleles are co-dominant.

Donor
The source of DNA in a genetic cross. For example, the transducing phage brought into a bacterial cell.

Downstream
A sequence located after a particular site relative to the direction of transcription and translation (i.e. located to the 3' side of a particular site). For example, the lacZ structural gene is located downstream of the lac promoter.

Double digestion
Cleavage of a DNA molecule with two different restriction endonucleases, either concurrently or consecutively.

Duplex DNA
A double-stranded DNA molecule.

Duplication
A region of DNA that is present in two copies. The DNA is present as an adjacent, direct repeat in tandem duplications. It is also possible for the duplicated DNA to be present at distant sites on a chromosome.

dUTPase
An enzyme which degrades dUTP to prevent the incorpation of dU into DNA.