Threose nucleic acid (TNA) is an artificial genetic polymer in which the natural five-carbon ribose sugar found in RNA has been replaced by an unnatural four-carbon threose sugar.Invented by Albert Eschenmoser as part of his quest to explore the chemical etiology of RNA, TNA has become an important synthetic genetic polymer (XNA) due to its ability to efficiently base pair with complementary sequences of DNA and RNA. However, unlike DNA and RNA, TNA is completely refractory to nuclease digestion, making it a promising nucleic acid analog for therapeutic and diagnostic applications.
TNA oligonucleotides were first constructed by automated solid-phase synthesis using phosphoramidite chemistry. Methods for chemically synthesized TNA monomers (phosphoramidites and nucleoside triphosphates) have been heavily optimized to support synthetic biology projects aimed at advancing TNA research.More recently, polymerase engineering efforts have identified TNA polymerases that can copy genetic information back and forth between DNA and TNA. TNA replication occurs through a process that mimics RNA replication. In these systems, TNA is reverse transcribed into DNA, the DNA is amplified by the polymerase chain reaction, and then forward transcribed back into TNA.
The availability of TNA polymerases have enabled the in vitro selection of biologically stable TNA aptamers to both small molecule and protein targets.Such experiments demonstrate that the properties of heredity and evolution are not limited to the natural genetic polymers of DNA and RNA. The high biological stability of TNA relative to other nucleic acid systems that are capable of undergoing Darwinian evolution, suggests that TNA is a strong candidate for the development of next-generation therapeutic aptamers.
The mechanism of TNA synthesis by a laboratory evolved TNA polymerase has been studied using X-ray crystallography to capture the five major steps of nucleotide addition.These structures demonstrate imperfect recognition of the incoming TNA nucleotide triphosphate and support the need for further directed evolution experiments to create TNA polymerases with improved activity. The binary structure of a TNA reverse transcriptase has also been solved by X-ray crystallography, revealing the importance of structural plasticity as a possible mechanism for template recognition.
John Chaput, a professor in the department of Pharmaceutical Sciences at the University of California, Irvine, has theorized that issues concerning the prebiotic synthesis of ribose sugars and the non-enzymatic replication of RNA may provide circumstantial evidence of an earlier genetic system more readily produced under primitive earth conditions. TNA could have been an early genetic system and a precursor to RNA.TNA is simpler than RNA and can be synthesized from a single starting material. TNA is able to transfer back and forth information with RNA and with strands of itself that are complementary to the RNA. TNA has been shown to fold into tertiary structures with discrete ligand-binding properties.
Although TNA research is still in its infancy, practical applications are already apparent. Its ability to undergo Darwinian evolution, coupled with its nuclease resistance, make TNA a promising candidate for the development of diagnostic and therapeutic applications that require high biological stability. This would include the evolution of TNA aptamers that can bind to specific small molecule and protein targets, as well as the development of TNA enzymes (threozymes) that can catalyze a chemical reaction. In addition, TNA is a promising candidate for RNA therapeutics that involve gene silencing technology. For example, TNA has been evaluated in a model system for antisense technology.
Nucleic acids are the biopolymers, or large biomolecules, essential to all known forms of life. The term nucleic acid is the overall name for DNA and RNA. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA ; if the sugar is derived from ribose as deoxyribose, the polymer is DNA.
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and DNA are nucleic acids. Along with lipids, proteins, and carbohydrates, nucleic acids constitute one of the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA, RNA is found in nature as a single strand folded onto itself, rather than a paired double strand. Cellular organisms use messenger RNA (mRNA) to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome.
The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage.
Peptide nucleic acid (PNA) is an artificially synthesized polymer similar to DNA or RNA.
Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, molecular cloning and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression, or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.
DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
Leslie Eleazer Orgel FRS was a British chemist. He is known for his theories on the origin of life.
Xenobiology (XB) is a subfield of synthetic biology, the study of synthesizing and manipulating biological devices and systems. The name "xenobiology" derives from the Greek word xenos, which means "stranger, alien". Xenobiology is a form of biology that is not (yet) familiar to science and is not found in nature. In practice, it describes novel biological systems and biochemistries that differ from the canonical DNA–RNA-20 amino acid system. For example, instead of DNA or RNA, XB explores nucleic acid analogues, termed xeno nucleic acid (XNA) as information carriers. It also focuses on an expanded genetic code and the incorporation of non-proteinogenic amino acids into proteins.
Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a specific chemical reaction, often but not always catalytic. This is similar to the action of other biological enzymes, such as proteins or ribozymes . However, in contrast to the abundance of protein enzymes in biological systems and the discovery of biological ribozymes in the 1980s, there is only little evidence for naturally occurring deoxyribozymes. Deoxyribozymes should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but do not catalyze a subsequent chemical reaction.
Aptamers are oligonucleotide 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 macromolecular drugs. Aptamers can be combined with ribozymes to self-cleave in the presence of their target molecule. These compound molecules have additional research, industrial and clinical applications.
Glycol nucleic acid (GNA), sometimes also referred to as glycerol nucleic acid, is a nucleic acid similar to DNA or RNA but differing in the composition of its sugar-phosphodiester backbone. GNA is chemically stable but not known to occur naturally. However, due to its simplicity, it might have played a role in the evolution of life.
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. These single-stranded DNA or RNA are commonly referred to as aptamers. Although SELEX has emerged as the most commonly used name for the procedure, some researchers have referred to it as SAAB and CASTing SELEX was first introduced in 1990. In 2015 a special issue was published in the Journal of Molecular Evolution in the honor of quarter century of the SELEX discovery.
Albert Jakob Eschenmoser (born 5 August 1925) is a Swiss organic chemist best known for his work on the synthesis of complex heterocyclic natural compounds, most notably vitamin B12. In addition to his significant contributions to the field of organic synthesis, Eschenmoser pioneered work in the Origins of Life (OoL) field with work on the synthetic pathways of artificial nucleic acids. Before retiring in 2009, Eschenmoser held tenured teaching positions at the ETH Zurich and The Skaggs Institute for Chemical Biology at The Scripps Research Institute in La Jolla, California as well as visiting professorships at the University of Chicago, Cambridge University, and Harvard.
Nucleic acid analogues are compounds which are analogous to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. An analogue may have any of these altered. Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties of the chain . Nucleic acid analogues are also called Xeno Nucleic Acid and represent one of the main pillars of xenobiology, the design of new-to-nature forms of life based on alternative biochemistries.
Masad J. Damha is a Canadian academic and nucleic acid researcher. He is Distinguished James McGill Professor of Chemistry at McGill University in Montreal, Quebec, Canada.
Nucleic acid templated chemistry (NATC), or DNA-templated chemistry, is a tool used in the controlled synthesis of chemical compounds. The main advantage of NAT-chemistry (NATC) is that it allows one to perform the chemical reaction as an intramolecular reaction. Two oligonucleotides or their analogues are linked via chemical groups to precursors of chemical compounds. The oligonucleotides recognize specific nucleic acids and are hybridized sterically close to each other. Afterwards the chemical active groups interact with each other to combine the precursors into a completely new chemical compound. NATC is usually used to perform synthesis of complex compounds without need to protect chemically active groups during the synthesis.
An L-ribonucleic acid aptamer is an RNA-like molecule built from L-ribose units. It is an artificial oligonucleotide named for being a mirror image of natural oligonucleotides. L-RNA aptamers are a form of aptamers. Due to their L-nucleotides, they are highly resistant to degradation by nucleases. L-RNA aptamers are considered potential drugs and are currently being tested in clinical trials.
A bridged nucleic acid (BNA) is a modified RNA nucleotide. They are sometimes also referred to as constrained or inaccessible RNA molecules. BNA monomers can contain a five-membered, six-membered or even a seven-membered bridged structure with a "fixed" C3'-endo sugar puckering. The bridge is synthetically incorporated at the 2', 4'-position of the ribose to afford a 2', 4'-BNA monomer. The monomers can be incorporated into oligonucleotide polymeric structures using standard phosphoamidite chemistry. BNAs are structurally rigid oligo-nucleotides with increased binding affinities and stability.
Xeno nucleic acids (XNA) are synthetic nucleic acid analogues that have a different sugar backbone than the natural nucleic acids DNA and RNA. As of 2011, at least six types of synthetic sugars have been shown to form nucleic acid backbones that can store and retrieve genetic information. Research is now being done to create synthetic polymerases to transform XNA. The study of its production and application has created a field known as xenobiology.
A sequence-controlled polymer is a macromolecule, in which the sequence of monomers is controlled to some degree. This control can be absolute but not necessarily. In other words, a sequence-controlled polymer can be uniform or non-uniform (Ð>1). For example, an alternating copolymer synthesized by radical polymerization is a sequence-controlled polymer, even if it is also a non-uniform polymer, in which chains have different chain-lengths and slightly different compositions. A biopolymer with a perfectly-defined primary structure is also a sequence-controlled polymer. However, in the case of uniform macromolecules, the term sequence-defined polymer can also be used.