Breaker Lab: Glossary of Terms

Glossary of Terms

	Designation for the catalytic strategy of in-line positioning for RNA transesterification. See also, Enzyme Speed Limits summary of our science.
Adaptive binding	Many RNA and DNA aptamers display induced fit or "adaptive binding." Many nucleic acids remain partially flexible and only adopt well-ordered structures in the presence of the cognate ligand, which makes them amenable to allosteric function.
Allosteric selection	An in vitro selection method for aptamers that is performed entirely in solution by virtue of the unique design of the population. A random sequence domain is inserted into a tolerant region of a catalytic RNA or DNA and the molecules recovered from selection demonstrate ligand-dependent catalytic function. Such a selection eliminates the need to immobilize the ligand on a column, and will not be subject to interference due to column immobilization.
Antisense	An RNA or DNA sequence that forms an uninterrupted double helix with another oligonucleotide, the ‘sense’ strand. Antisense technology is used to regulate genetic expression by binding cellular (sense) mRNAs in order to reduce their stability or availability for translation.
Aptamer	An RNA or DNA sequence that folds into a 3-dimensionall shape that specifically binds a ligand.
	Designation for the catalytic strategy of non-bridging phosphate oxygen charge neutralization for RNA transesterification. See also, Enzyme Speed Limits summary of our science.
	Designation for the catalytic strategy of 5´-O leaving groups activation for RNA transesterification. See also, Enzyme Speed Limits summary of our science.
Catalyst	An agent that accelerates the rate of a chemical reaction, in some cases many order of magnitude above the uncatalyzed rate. A catalyst participates in the reaction but is not consumed. The agent may be a simple ion or compound or a large macromolecule. See also, enzyme.
Catalytic antisense	A term used to indicate a ribozyme or deoxyribozyme used in the application of therapeutic mRNA cleavage.
Cofactor	An ion or molecule whose presence is essential to the activity of a ribozyme or deoxyribozyme. Presumably, the ion or molecule is held in the active site of the enzyme and used directly for catalysis, though the term cofactor is often used even when mechanism has not been rigorously tested.
Communication module	A sequence obtained by in vitro selection that relays a conformational status among domains within a molecule. For example, the binding of a ligand to an aptamer domain can be used to regulate the activity of a catalytic domain in the same molecule via a communication module. See also, Nucleic Acid Engineering tutorial.
	Designation for the catalytic strategy of 2´-O nucleophile activation for RNA transesterification. See also, Enzyme Speed Limits summary of our science
Deoxyribozyme	A specific sequence of DNA that catalyzes a chemical reaction. Known deoxyribozymes all contain significant regions of single-stranded and other non-duplex structure as would be expected to be required for the formation of a topologically diverse active site. There are no deoxyribozymes known in nature. See also, enzyme and ribozyme.
Enzyme	A macromolecule (e.g. RNA, DNA, or protein) that accelerates the rate of a chemical reaction, typically many orders of magnitude above the uncatalyzed rate. Enzymes are a subset of catalysts.
Group I Intron	One of a pair of the first ribozymes discovered. The Nobel Prize in Chemistry was awarded to Thomas Cech and Sidney Altman in 1989 for their respective discoveries of the Group I intron ribozyme and the RNase P ribozyme.
In vitro evolution	Conceptually identical to in vitro selection. Molecules in an in vitro evolution experiment are subjected to alternating cycles of selection – allowing survival and amplification of the ‘fittest’ molecules – analogous to reproduction. See also, In Vitro Evolution tutorial and in vitro selection.
In vitro selection	Conceptually identical to in vitro evolution. The distinction reflects whether mutations are (evolution) or are not (selection) deliberately introduced. In practice though, many selections pass through so many cycles of amplification that mutations become introduced through inherent error of the polymerization. See also, in vitro evolution tutorial.
Ligand	An ion or molecule that is bound (held in close contact) by another, typically much larger, molecule.
Macromolecule	A molecule that is produced by cells or by chemical means by repeatedly joining together subunits into a long chain. Also called biological polymers, the macromolecules of interest on this site are RNA, DNA, and protein.
Ribosome	The ribonucleoprotein machine responsible for most biological protein synthesis. Recent high-resolution structural evidence supports older biochemical evidence that the catalytic heart of this machine is RNA and that the ribosome is actually a ribozyme.
Riboswitch	RNA genetic control elements that influence transcription termination or translation initiation by conformation rearrangement of the RNA in response to direct metabolite binding.
Ribozyme	A specific sequence of RNA (natural or synthetic) that catalyzes a chemical reaction, presumably by folding into a defined 3-dimensional shape containing the enzymatic active site. See also, enzyme and deoxyribozyme.
RNAi	The process whereby short duplexes of RNA are used in nature for genetic regulation.
RNase P	One of a pair of the first ribozymes discovered. The Nobel Prize in Chemistry was awarded to Sidney Altman and Thomas Cech in 1989 for their respective discoveries of the RNase P ribozyme and the Group I intron ribozyme.
Selective pressure:	Pools subjected to in vitro evolution can be required to perform desired functions such as: catalyzing a (self-modifying) chemical reaction; binding a target analyte; or relaying the status of domains within a multi-functional molecule (selection for communication modules). The experimental design provides a way to physically separate the successful molecules prior to amplification. This has been accomplished through partitioning to a surface, enrichment of molecules of a new molecular size, or increased susceptibility to a secondary reaction.
3-dimensional structure	The folded shape of a macromolecule. Though macromolecules are created as linear chains, the nature of these molecules is to collapse into compact shapes determined by the sequence of the subunits. See also, RNA as a Living Molecule tutorial.
Transcription termination (intrinsic or factor independent)	The process of causing RNA polymerases to halt addition of ribonucleotides to a growing RNA chain in response to a structural element in the nascent RNA chain. This structural element is a hairpin followed by several uridine residues. Some riboswitches are known to control this process.

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