The RNA Ligase ribozyme was the first of several types of synthetic ribozymes produced by in vitro

In vitro

In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...

 evolution

Evolution

Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...

 and selection

Selection

In the context of evolution, certain traits or alleles of genes segregating within a population may be subject to selection. Under selection, individuals with advantageous or "adaptive" traits tend to be more successful than their peers reproductively—meaning they contribute more offspring to the...

 techniques. They are an important class of ribozymes because they catalyze the assembly of RNA

RNA

Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 fragments into phosphodiester RNA polymers, a reaction required of all extant nucleic acid

Nucleic acid

Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...

 polymerases and thought to be required for any self-replicating molecule. Ideas that the origin of life may have involved the first self-replicating molecules being ribozymes are called RNA World hypotheses. Ligase ribozymes may have been part of such a pre-biotic RNA world.

In order to copy RNA, fragments or monomers (individual building blocks) that have 5'-triphosphates

Nucleotide

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...

 must be ligated together. This is true for modern (protein-based) polymerases

RNA polymerase

RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...

, and is also the most likely mechanism by which a ribozyme self-replicase in an RNA world might function. Yet no one has found a natural ribozyme that can perform this reaction.

In vitro evolution and selection

RNA in vitro evolution

Directed evolution

thumb|250px|right|An example of a possible round to evolve a protein based fluorescent sensor for a specific analyte using two consecutive FACS sortings...

 or SELEX

Systematic Evolution of Ligands by Exponential Enrichment

SELEX , also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands....

 enables the artificial evolution and selection of RNA

RNA

Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 molecules that possess a desired property, such as binding affinity for a particular ligand

Ligand

In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...

 or an activity such as that of an enzyme

Enzyme

Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

 or catalyst. The first such selections involved isolation of various aptamer

Aptamer

Aptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule. Aptamers are usually created by selecting them from a large random sequence pool, but natural aptamers also exist in riboswitches. Aptamers can be used for both basic research and clinical purposes as...

s that bind to small molecules. The first catalytic RNAs produced by in vitro evolution were RNA

RNA

Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....

 ligases, catalytic RNAs that join two RNA fragments to produce a single adduct

Adduct

An adduct is a product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species...

.

RNA test tube (in vitro) evolution and selection

Systematic Evolution of Ligands by Exponential Enrichment

SELEX , also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands....

 has thus enabled several research groups to discover RNA sequences that can in fact catalyze the required chemical reaction for 5'-triphosphate RNA fragment ligation, and one group has even produced a functional RNA polymerase ribozyme.

The L1 ligase

Michael Robertson and Andrew Ellington evolved a ligase ribozyme that performs the desired 5'-3' RNA assembly reaction, and called this the L1 ligase. To better understand the details of how this ribozyme folds into a structure that permits it to catalyze this fundamental reaction, the X-ray crystal structure

X-ray crystallography

X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...

has been solved. The structure is composed of three helical stems called stem A, B and C, that connect at a three helix junction.