Radioactive suicide
The death of cells due to incorporation of a radioactive substrate with high specific activity. Radioactive suicide can be used as a technique to select for mutants that are unable to incorporate a particular substrate.

Random primers
A set of short oligonucleotides with variable sequences. Within a population of random oligonucleotides, some will anneal to complementary sequences in a DNA or RNA template. Use of random primers to initiate DNA synthesis in the presence of a radiol abeled (or chemiluminescent) dexoynucleotide (dNTP) will yield probes representing the sequences found in the template DNA. The labeled probes can then be used to identify other sequences homologous to this DNA (e.g. by Southern blotting).

Read-through
Failure to stop transcription at a normal termination signal.

Reading frame
The sequence of nucleotides which is read as consecutive triplets during translation of mRNA into protein. A sequence of codons that continues without encountering a stop codon is called an open reading frame (ORF). For a sequence of double-stranded DNA there are six possible reading frames; three in the forward direction, and three in the reverse direction. A sequence of DNA will often have one ORF, but in some cases a sequence of DNA will include overlapping ORFs that encode distinct polypeptides.

Reciprocal crosses
Pairs of genetic crosses which in one case DNA from strain #1 is transferred into strain #2 and in the second case the strain #2 is used as a donor to transfer the same region into strain #1. For example

Cross A = donor (pro::Tn10) x recipient (pro+)

Cross B = donor (pro+) x recipient (pro::Tn10)

Reciprocal recombination
A precise exchange of genetic information like that expected for a simple cut, exchange, and rejoin mechanism. That is, a region of DNA simply moves from the donor molecule to the recipient molecule in exchange for the identical region from the recipient molecule.

RecA protein
The protein encoded by the recA gene which is essential for homologous recombination. The RecA protein is also involved in the induction of the SOS response and the induction of lambda prophage in response to DNA damaging agents.

Recessive
A genetic trait that is not expressed in a heterozygous or partially heterozygous cell.

Recombinant DNA
A molecule of DNA in which a DNA fragment from a different source has been inserted.

Recombinase
An enzyme that catalyzes genetic recombination.

Recombination
Genetic exchange resulting from a cross-over between two different DNA molecules or different regions of a DNA molecule. See General recombination, Illegitimate recombination and Sitespecific recombination.

Recombination frequency
The number of recombinants divided by the total number of progeny. The recombination frequency is proportional to the physical distance between two genetic markers, and thus recombination frequencies can be used to draw genetic maps showing the relat ive distance between genetic markers. Note that often the coinheritance frequency -- the probablity that recombination did NOT occur between two markers is used instead of the recombination frequency.

Recombineering ("Recombination-mediated genetic engineering")
A term coined by Don Court to describe a method for vector construction based on homologous recombination in E. coli using lambda phage recombination proteins exo, bet, and gam. This process allows homologous recombination between much shorter DNA sequences than the E. coli homologous recombination system. See http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/in-vitro-genetics/red-swap.html.

Redundant genes
Multiple copies of a gene or different genes with the same function.

Regulon
A group of genes or operons located at different positions on the chromosome but respond to a common regulatory protein.

Release factors (RF)
Proteins that facilitate the termination of translation. Translation termination occurs when a ribosome encounters one of the three stop codons (UAA, UAG, or UGA). These codons are not recognized by a tRNA but by protein release factors. RF-1 recognizes UAA and UAG, RF-2 recognizes UAA and UGA. RF-3 stimulates the activity of RF-1 and RF-2. Interaction of the RF with a stop codon causes the peptidyl transferase activity of the ribosome to catalyze the hydrolysis of the ester bond between the tRNA and the polypeptide chain, releasing the polypeptide chain and resulting in dissociation of the ribosome.

Replica plating
A technique for transferring an identical pattern of bacterial colonies from one petrie plate (the master plate) to a series of other plates containing different media. A plate containing bacterial colonies is pressed against a cylindrical block covered with velveteen, resulting in the transfer of many of the bacteria from each colony onto the corresponding position on the velveteen. Then a series of sterile plates are sequentially pressed against the velveteen to transfer cells from the velveteen to the corresponding position on each petrie plate. After incubation, if the cells can grow on the particular medium in a plate colonies will appear at identical positions on each plate. Typically about 10 replica plates can be made from each master plate with about 200 isolated colonies on the master plate. Thus, it is possible to quickly screen a large number of colonies for a variety of phenotypic characteristics.

Replication
The process of duplicating a DNA molecule.

Replication fork
The region on a replicating doublestranded DNA molecule where synthesis of new DNA is taking place. The replicating fork produces a Yshaped region in the DNA molecule where the two strands have separated and replication is taking place.

Replication restart
An event that occurs when replication forks that collapse or disintegrate spontaneously do not progress to the completion of the chromosome; the replication fork is reasembled at the site of its collapse.

Replicative transposition
The insertion of a transposable element at a new location without loss from the original location.

Replicon
A DNA molecule that is able to initiate its own replication. A replicon must have an origin of replication and usually also has the necessary regulatory information required for the proper initiation of DNA replication.

Replicon fusion
The integration of one replicon into another to form a single replicon. May occur by recombination between homologous regions of two replicons or by formation of a cointegrate during transposition of a transposable element located on one of the repli cons.

Reporter gene
A gene which can be placed downstream of a promoter and expression of the gene followed by a relatively easy assay (often a colorimetric assay). See operon and gene fusions.

Repression
Switching off the expression of a gene or a group of genes in response to a chemical or other stimulus.

Repressor
A gene product that negatively regulates gene expression. Usually refers to a DNA-binding protein that inhibits transcription under certain conditions. Transcriptional repressors typically decrease the transcription of certain other genes by specifically binding to operator sites -- one or more short DNA sequences located upstream of the structural gene. Regulation of repression is usually modulated by a ligand which binds to the repressor protein and alters its DNA-binding properties. DNA-binding may be increased by association with a co-repressor or DNA-binding may be decreased by association with an inducer.

Resistance transfer factor (RTF)
The component of an R-plasmid that encodes the ability to conjugate and to transfer DNA.

Resolvase
An enzyme which resolves a co-integrate molecule into its two component replicons.

Response regulator
A regulatory protein that responds to sensor protein of a "two-component" regulatory system. Interaction with the transmitter domain of the sensor protein, leads to the phosphorylation or dephosphorylation of an aspartate residue on the response regulator. The modified protein regulates gene expression in response to the changes in the environment.

Restriction
The cleavage of double-stranded DNA by an endonuclease (restriction enzyme). The restriction enzyme distinguishes between self and foreign DNA based upon the modification of its DNA-binding site (for example, by methylation).

Restriction analysis
Determination of the number and sizes of the DNA fragments produced when a particular DNA molecule is cut with a particular restriction endonuclease.

Restriction endonuclease
An endonuclease cuts doublestranded DNA by binding to specific sites, in many cases arranged in palindromes. Several different classes of restriction endonucleases can be differentiated based upon their binding and cleavage sites and their required cofactors. Although restriction endonucleases have specific recognition sites, cleavage may occur at specific or random sites depending on the class of the endonuclease. Also called restriction enzymes.

Restriction fragment length polymorphism (RFLP)
A mutation that results in a detectable change in the pattern of fragments obtained when a DNA molecule is cut with a restriction endonuclease.

Restriction map
A map showing the positions of different restriction sites in a DNA molecule.

Restriction-modification
The modification of host DNA to prevent cutting by a restriction endonuclease (see restriction endonuclease). The modification is often via methylation of a specific restriction site sequence.

Restriction site
A DNA sequence recognized and cleaved by a restriction endonuclease. Restriction sites are often 4 to 6 bp, but some sites are 8 bp or longer. The presence or absence of specific nucleotide modifications (e.g. methylation) determines whether the restriction endonuclease cleaves at its cognate restriction site.

Restrictive conditions
The particular environmental conditions which do not allow growth of a conditional lethal mutant but result in the expression of the mutant phenotype.

Retroregulation
The effect of a downstream RNA sequence upon the expression of an upstream sequence. First used to describe the regulation of the phage lambda xis gene (see http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/phage/int-xis.html)

Retrotransposon
A genetic element that transposes to a new location in DNA by first making an RNA copy of itself, then making a DNA copy of this RNA with a reverse transcriptase, and then inserting the DNA copy into the target DNA.

Reverse genetics
An approach where a cloned gene with an unknown function is used to disrupt the corresponding chromosomal gene to examine the resulting phenotype.

Reverse transcriptase
An enzyme produced by retroviruses that can synthesize a strand of DNA complimentary to an RNA template. (Reverse transcriptase can also synthesize DNA from a DNA template.) Used to make cDNA clones from mRNA.

Reversion
Any mutation that restores the wild-type phenotype of a mutant.

R-factor
A transmissible plasmid that carries genes coding for resistance to several different antibiotics. Also called R-plasmid.

RFLP
See Restriction fragment length polymorphism.

Rho factor
A protein which catalyzes transcription termination at certain sites or when an extended stretch on nontranslated, unstructured RNA is present. See Rho dependent polarity .

Ribosomal (rRNA)
An RNA molecule that forms part of the structure of a ribosome.

Ribosome
An RNA-protein complex responsible for the correct positioning of mRNA and charged tRNAs allowing proper alignment of amino acids during protein synthesis.

Ribosome binding site
A short nucleotide sequence upstream of a gene which forms the site on the mRNA molecule where the ribosome binds. (Also called a Shine-Delgarno sequence.)

Rich medium
A growth medium in which not all the components have been identified. Most "rich" media have a variety of complex, undefined componants.

rII locus
A region from phage T4 that determines whether this phage can grow on E. coli K or B strains. Fine structure genetic mapping of the rII locus by Sydney Benzer first unveiled a variety of important facets of gene structure and function.

RNA phage
A phage that carries RNA as its genetic material. Some examples include phage MS2 and Q.

RNA polymerase (RNAP)
An enzyme complex that polymerizes RNA from ribonucleotides (NTPs), using one strand of DNA as template (hence called "DNA-dependent RNA polymerase). The core RNAP from E. coli is composed of five subunits: 2 alpha subunits, beta, beta', and omega. Upon binding another subunit called sigma, RNAP is called a holoenzyme. The sigma subunit (or sigma factor) reduces the nonspecific affinity of RNAP for DNA and increases the specific binding to certain promoter sequences. A variety of different sigma subunits exist, each promoting RNAP binding to different promoters under specific physiological conditions.

Rolling circle (sigma) replication
A type of DNA replication where a replication fork moves around a circular DNA molecule, producing a single-stranded concatamer (much like the way toilet paper peels off the roll). The resulting single-stranded DNA may become double-stranded by the synthesis of a complementary strand.

RNase
An enzyme that hydrolyses RNA molecules.

RPM
Revolutions per minute. Often used to describe the velocity of a centrifuge.