Hairpin
A region of single-stranded DNA or RNA that can form base pairs between complementary sequences. For example the sequence 5'...GACGTGNNNNNCTGCAC...3' could form a short double-stranded region between the sequences shown while any noncomplementary intervening sequences (shown as N to indicate any nucleotides) would form a single-stranded loop. Also called a "stem and loop" structure or a cruciform structure.

Half-site
The DNA sequence recognized by a dimeric protein is composed of two half-sites, with each half-site bound by a monomer. Half-sites are often inverted repeats, and more rarely direct repeats.

Hand-cuffing
A process that leads to replication inhibition in plasmids containing iterons. When a sufficiently high copy number of plasmid molecules accumulate, the replication initiator protein binds to the iteron sequences on two plasmids simultaneously, thereby inactivating both initiation of DNA replication of both plasmids.

Haploid
Only one copy of each chromosome per cell. (Prokaryotes are haploid, although more than one copy of a chromosome may be transiently present in the cell, depending on the rate of DNA replication and the growth rate.)

Headful packaging
The packaging (filling) of a viral capsid with viral nucleic acid until the capsid is full. Headful packaging is based upon the size of nucleic acid stuffed into the capsid rather than the recognition of specific sites on the viral genome. For an example, see the link on P22 packaging.

Heat shock response
A global regulatory response resulting in increased or decreased expression of a number of genes in response to injury by heat, osmotic change and certain other forms of stress.

Helper phage
A phage that is introduced into a host cell in to provide functions needed for replication, morphogenesis, or packaging of a mutant (defective) phage.

Helicases
Proteins that unwind the DNA double helix.

Hemimethylation
Double stranded DNA in which only one strand is methylated at a particular site. For example, at GATC sites in E. coli the A residues on both strands are methylated by DAM methylase but, because DAM methylase lags behind DNA polymerase, immediately after DNA replication only the parental strand is methylated.

Heteroduplex DNA
A double-stranded DNA molecule formed by annealing complementary (or partially complementary) single-stranded DNA from two different sources.

Heteroimmune phage
A phage that is not sensitive to the repression of lytic development by another prophage in the infected cell.

Heterokaryosis
The process whereby cells fuse to form a multinucleate cell containing nuclei from different parents. Nuclear fusion does not take place.

Heterologous
(i) DNA regions coding for the same function but with differences in their nucleotide sequences; (ii) DNAs which originate from different species.

Heterologous probe
The use of a labelled nucleic acid molecule to identify related molecules by hybridization probing.

Heterotrophic
The ability of an organism to use an organic molecule as carbon source.

Heterozygote
A diploid or partially diploid organism with different alleles of one or more particular genes.

Hfr (high frequency of recombination)
A cell in which the F-factor has integrated into a specific location in the chromosome, causing it to act as a highfrequency donor of chromosomal genes in crosses with F- cells.

HFT lysate
A lysate from a lysogenic phage that includes a substantial proportion of transducing fragments. For example, induction of a dilysogen that carries an insertion of both wild-type phage and a defective, specialized transducing phage will often yield about 50% transducing particles.

Histone
A basic protein from eukaryotes (or Archae) which binds to DNA, forming nucleosomes, and packaging the DNA into chromatin.

Histone-like proteins
Proteins from bacteria which bind to DNA, and compact the DNA.

Holin
A phage encoded lysis protein that forms pores ("holes") in the cytoplasmic membrane and allows release of an enzyme that degrades peptidoglycan (e.g. lysozyme), facilitating lysis of the host cell.

Holliday junction
The cruciform structure formed as an intermediate in homologous genetic recombination.

Holoenzyme
A complex containing all of the subunits required for a functional enzyme. Used to describe enzymes composed of many different protein subunits. For example, RNA polymerase holoenzyme is composed of six subunits: 2 alpha subunits, beta, beta', omega, and sigma.

Homoduplex
A molecule of double-stranded nucleic acid where the two strands have exactly complementary base sequences.

Homoimmune
Expression of a repressor by a lysogenic phage that prevents successful infection by another phage with the same repressor-operator recognition. For example, lambda lysogens are resistant to superinfection by another lambda phage because upon entering the lysogen, cI produced by the prophage turns off gene expression from PL and PR on the incoming phage.

Homologous
Nucleic acid molecules with the same base sequence except for minor differences in alleles; (ii) nucleic acid molecules originating from strains of the same species, thus having at least long stretches of identical DNA base sequences; (iii) gene or protein families having a recognizable common evolutionary origin.

Homologous recombination
The physical exchange of DNA between two homologous DNA molecules. Requires the RecA protein in enteric bacteria. Also called general recombination.

Homology
(i) Sequence identity between two nucleotide sequences. (ii) Genetic relatedness between two sequences of common ancestry. Commonly confused with sequence similarity. For example, 85% similarity means that 85 nucleotide positions out of 100 are identical in the two polynucleotides.

Homopolymer tailing
Attachment of a sequence of identical nucleotides (e.g. TTTTT) to the end of a nucleic acid molecule. Typically single-stranded homopolymer extensions are added to the ends of a double-stranded DNA molecule.

Homothallism
A process occurring in some yeasts and other fungal strains where haploid spores formed during meiosis undergo self-diploidization due to the switching of mating type by some of the progeny of the spore.

Homozygous
A cell or organism where the same allele is carried by each member of a pair of homologous chromosomes.

Horseradish peroxidase
An enzyme that can be complexed to DNA for use in some non-radioactive DNA labeling procedures.

Hostcontrolled restriction
A mechanism by which some bacteria degrade unmodified foreign DNA by a restriction endonuclease that recognizes a specific nucleotide sequence.

Host-range
The strain or species specificity of a bacteriophage, plasmid, or pathogen.

Hot spot
A region that is especially susceptible to mutations. Mutations occur at such sites at a much higher frequency than most other positions in the genome.

Hybridization probe
A labelled nucleic acid molecule that can be used to identify complementary or homologous molecules through the formation of stable base-paired hybrids.

Hybridization
A technique where a denatured (single-stranded) nucleotide chain (DNA or RNA) is allowed to pair with another single-stranded nucleotide chain. Hybridization will only occur if the two sequences are sufficiently related for a substantial number of hydrogen bonds to form between their complementary bases.

Hydroxylamine
NH2OH

-- A mutagen that reacts with C residues, producing a modified base (N4-hydroxyC) that pairs with A instead of G, and hence resulting in GC to AT transition mutations.

Hydroxymethyl cytosine
A modification of cystine residues. This modification is typical of some phage DNA. The modified DNA is resistant to certain restriction endonucleases.

Hyphae
Multicellular filaments formed during the vegetative reproduction of fungi or actinomycetes.