The arrangement of polysaccharide side chains on the LPS of Gram-negative bacteria. Serves as the receptor for some types of phage.

Ochre codon
The UAA stop codon.

Ochre mutation
A change in a codon to create the nonsense codon UAA (the ochre codon).

Okasaki fragments
Short DNA fragments of about 1000-2000 nucleotides long formed during DNA replication of the lagging strand by discontinuous replication of DNA. Okasaki fragments are later joined together by ligation.

A short sequence of polynucleotide. Oligonucleotides with a defined sequence can synthesized in vitro for use for a variety of techniques, including PCR, DNA sequence analysis, hybridization, and site-directed mutagenesis. The length of an oligonucleotide is described as a #-mer -- for example, an oligonucleotide with 20 nucleotides would be called a 20-mer).

Oligonucleotide-directed mutagenesis
An in vitro mutagenesis technique that involves the use of a synthetic oligonucleotide to introduce the predetermined nucleotide alteration into the gene to be mutated.

This suffix indicates the complete collection of the subunits described in the word stem. For example, genome indicates the entire haploid complement of genetic material in an organism, pproteome indicates the entire set of proteins expressed by an organism, etc. [Source: J. Lederberg and A. McCray (2001) The Scientist 15:8]

One-step growth curve
A plot of the production of lytic growth of a virus vs time. An excess of bacteria is infected with virus. There is an initial drop in the number of plaque forming units (PFU) of virus due to entry of the virus into cells and release of the viral nucleic acid. This is followed by a period of time called the eclipse phase where viral proteins and nucleic acid are reproduced but no viable virus is produced. After this period mature viruses are assembled and released from the cell. The "burst size" is the number of virus particles released from the cell divided by the number of virus particles initially added. The one-step growth curve is terminated after the first round of infection.

Opal codon
The UGA stop codon.

Opal mutation
A change in a codon to create the nonsense codon UGA (the opal codon).

Open reading frame (ORF)
A stretch of DNA which potentially codes for protein. A length of DNA not interrupted by stop codons. A sequence of in frame codons preceded by a translational initiation codon and terminated by a chain termination triplet.

The non-supercoiled conformation taken up by a circular double-stranded DNA molecule when one or both polynucleotides carry nicks.

The DNA sequence where a repressor protein reversibly binds to regulate the activity of one or more closely linked structural genes.

A sequence of adjacent genes read as a single, polycistronic mRNA. Changes in the level of transcription thus affects all of the genes in an operon, so such genes are often coordinately regulated. Includes both the structural genes, and the operator and promoter sequences that control them.

Operon fusion
A construct that places the coding region of a gene downstream of the promoter for another gene, such that transcription of the downstream gene initiates from this new promoter but translation of the downstream gene occurs from its own translation start site. For a more detailed description, see Operon and Gene fusions. Sometimes called a transcriptional fusion or fusion.

Origin of replication (ori)
The nucleotide sequence where DNA replication is initiated. Determines the specific position on a DNA molecule where DNA replication begins.

Orthogonal field alternating gel electrophoresis (OFAGE)
A gel electrophoresis technique that employs a pulsed electric field to achieve separation of very large molecules of DNA.

A gene present in multiple species that descended from a unique ancestral gene, when the relative divergence in different species is comparable to the overall difference between the species. Such genes provide useful tools for constructing phylogenetic trees (for examples, see http://www.ncbi.nlm.nih.gov/COG/).

Outer membrane
The lipopolysaccharide (LPS) containing layer, containing some proteins, which surrounds the cytoplasmic membrane and forms the outermost layer of most Gram-negative bacteria. The outer membrane usually confers resistance to many detergents and contains the receptor sites for certain phage.

Overlapping genes
Two genes whose nucleotide sequences partially overlap. The two genes may be translated in different reading frames with the 3' end of one structural gene overlaping with the 5' end of another structural gene, the two genes may be translated in different reading frames with one structural gene located entirely within the other, or the two genes may be translated in the same reading frame with one structural gene located entirely within the other.

Overproduction suppression
Suppression of a mutant phenotype by expression of a protein at high levels due to a regulatory mutation or expression from a multicopy plasmid. Typically overexpression suppression is used to describe the partial or full restoration of the wild-type phenotype by high levels of a protein with weak activity, either the corresponding leaky mutant protein or another gene product with weak activity.