Threose nucleic acid

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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nucleic acid (TNA) is an artificial genetic polymer in which the natural five-carbon ribose sugar found in RNA has been replaced by an unnatural four-carbon threose sugar. [1] Invented by Albert Eschenmoser as part of his quest to explore the chemical etiology of RNA, [2] TNA has become an important synthetic genetic polymer (XNA) due to its ability to efficiently base pair with complementary sequences of DNA and RNA. [1] The main difference between TNA and DNA/RNA is their backbones. DNA and RNA have their phosphate backbones attached to the 5' carbon of the deoxyribose or ribose sugar ring, respectively. TNA, on the other hand, has its phosphate backbone directly attached to the 3' carbon in the ring, since it does not have a 5' carbon. This modified backbone [3] makes TNA, unlike DNA and RNA, completely refractory to nuclease digestion, making it a promising nucleic acid analog for therapeutic and diagnostic applications. [4]

Contents

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. [5] More recently, polymerase engineering efforts have identified TNA polymerases that can copy genetic information back and forth between DNA and TNA. [6] [7] 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. [8] [9] [10] Such experiments demonstrate that the properties of heredity and evolution are not limited to the natural genetic polymers of DNA and RNA. [11] 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. [12] 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. [13]

Pre DNA system

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.{{subst: cn }} TNA could have been an early genetic system and a precursor to RNA. [14] 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. [8]

Commercial applications

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. [15]

See also

Related Research Articles

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Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is deoxyribose, a variant of ribose, the polymer is DNA.

<span class="mw-page-title-main">Nucleotide</span> Biological molecules constituting nucleic acids

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.

<span class="mw-page-title-main">RNA</span> Family of large biological molecules

Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself or by forming a template for the production of proteins. RNA and deoxyribonucleic acid (DNA) are nucleic acids. The nucleic acids constitute one of the four major macromolecules essential for all known forms of life. RNA is assembled as a chain of nucleotides. 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.

<span class="mw-page-title-main">RNA world</span> Hypothetical stage in the early evolutionary history of life on Earth

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. Alexander Rich first proposed the concept of the RNA world in 1962, and Walter Gilbert coined the term in 1986.

<span class="mw-page-title-main">Nucleoside</span> Any of several glycosylamines comprising a nucleobase and a sugar molecule

Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase and a five-carbon sugar whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building blocks of DNA and RNA.

<span class="mw-page-title-main">Peptide nucleic acid</span> Biological molecule

Peptide nucleic acid (PNA) is an artificially synthesized polymer similar to DNA or RNA.

In polymer science, the polymer chain or simply backbone of a polymer is the main chain of a polymer. Polymers are often classified according to the elements in the main chains. The character of the backbone, i.e. its flexibility, determines the properties of the polymer. For example, in polysiloxanes (silicone), the backbone chain is very flexible, which results in a very low glass transition temperature of −123 °C. The polymers with rigid backbones are prone to crystallization in thin films and in solution. Crystallization in its turn affects the optical properties of the polymers, its optical band gap and electronic levels.

<span class="mw-page-title-main">Ribonucleotide</span> Nucleotide containing ribose as its pentose component

In biochemistry, a ribonucleotide is a nucleotide containing ribose as its pentose component. It is considered a molecular precursor of nucleic acids. Nucleotides are the basic building blocks of DNA and RNA. Ribonucleotides themselves are basic monomeric building blocks for RNA. Deoxyribonucleotides, formed by reducing ribonucleotides with the enzyme ribonucleotide reductase (RNR), are essential building blocks for DNA. There are several differences between DNA deoxyribonucleotides and RNA ribonucleotides. Successive nucleotides are linked together via phosphodiester bonds.

<span class="mw-page-title-main">Locked nucleic acid</span> Biological molecule

A locked nucleic acid (LNA), also known as bridged nucleic acid (BNA), and often referred to as inaccessible RNA, is a modified RNA nucleotide in which the ribose moiety is modified with an extra bridge connecting the 2' oxygen and 4' carbon. The bridge "locks" the ribose in the 3'-endo (North) conformation, which is often found in the A-form duplexes. This structure provides for increased stability against enzymatic degradation. LNA also offers improved specificity and affinity in base-pairing as a monomer or a constituent of an oligonucleotide. LNA nucleotides can be mixed with DNA or RNA residues in a oligonucleotide.

<span class="mw-page-title-main">Leslie Orgel</span> British chemist

Leslie Eleazer Orgel FRS was a British chemist. He is known for his theories on the origin of life.

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<span class="mw-page-title-main">Aptamer</span> Oligonucleotide or peptide molecules that bind specific targets

Aptamers are oligomers of artificial ssDNA, RNA, XNA, or peptide that bind a specific target molecule, or family of target molecules. They exhibit a range of affinities, with variable levels of off-target binding and are sometimes classified as chemical antibodies. Aptamers and antibodies can be used in many of the same applications, but the nucleic acid-based structure of aptamers, which are mostly oligonucleotides, is very different from the amino acid-based structure of antibodies, which are proteins. This difference can make aptamers a better choice than antibodies for some purposes.

<span class="mw-page-title-main">Glycol nucleic acid</span> Polymer similar to DNA

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, using propylene glycol in place of ribose or deoxyribose. 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.

<span class="mw-page-title-main">Systematic evolution of ligands by exponential enrichment</span> Technique for producing oligonucleotides that specifically bind to a target

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 discovery of SELEX.

<span class="mw-page-title-main">Albert Eschenmoser</span> Swiss organic chemist (1925–2023)

Albert Jakob Eschenmoser (5 August 1925 – 14 July 2023) was 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.

<span class="mw-page-title-main">Nucleic acid analogue</span> Compound analogous to naturally occurring RNA and DNA

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<span class="mw-page-title-main">Xeno nucleic acid</span> Synthetic nucleic acid analogues

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References

  1. 1 2 Schöning, K. U. et al. Chemical etiology of nucleic acid structure: the a-threofuranosyl-(3'-->2') oligonucleotide system. Science290, 1347-1351, (2000)
  2. ↑ Eschenmoser, A. Chemical etiology of nucleic acid structure. Science284, 2118-2124, (1999).
  3. ↑ Dunn, Matthew R.; Larsen, Andrew C.; Zahurancik, Walter J.; Fahmi, Nour Eddine; Meyers, Madeline; Suo, Zucai; Chaput, John C. (2015-04-01). "DNA Polymerase-Mediated Synthesis of Unbiased Threose Nucleic Acid (TNA) Polymers Requires 7-Deazaguanine To Suppress G:G Mispairing during TNA Transcription". Journal of the American Chemical Society. 137 (12): 4014–4017. doi:10.1021/ja511481n. ISSN   0002-7863. Archived from the original on 2022-10-26. Retrieved 2023-09-17.
  4. ↑ Culbertson, M. C. et al. Evaluating TNA stability under simulated physiological conditions. Bioorg. Med. Chem. Lett.26, 2418-2421, (2016).
  5. ↑ Sau, S. P., Fahmi, N. E., Liao, J.-Y., Bala, S. & Chaput, J. C. A scalable synthesis of α-L-threose nucleic acid monomers. J. Org. Chem.81, 2302-2307, (2016).
  6. ↑ Larsen, A. C. et al. A general strategy for expanding polymerase function by droplet microfluidics. Nat. Commun.7, 11235, (2016).
  7. ↑ Nikoomanzar, A., Vallejo, D. & Chaput, J. C. Elucidating the Determinants of Polymerase Specificity by Microfluidic-Based Deep Mutational Scanning. ACS Synth. Biol.8, 1421-1429, (2019).
  8. 1 2 Yu, H., Zhang, S. & Chaput, J. C. Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor. Nat. Chem.4, 183-187, (2012).
  9. ↑ Mei, H. et al. Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues. J. Am. Chem. Soc.140, 5706-5713, (2018).
  10. ↑ Rangel, A. E., Chen, Z., Ayele, T. M. & Heemstra, J. M. In vitro selection of an XNA aptamer capable of small-molecule recognition. Nucleic Acids Res.46, 8057-8068, (2018).
  11. ↑ Pinheiro, V. B. et al. Synthetic genetic polymers capable of heredity and evolution. Science336, 341-344, (2012).
  12. ↑ Chim, N., Shi, C., Sau, S. P., Nikoomanzar, A. & Chaput, J. C. Structural basis for TNA synthesis by an engineered TNA polymerase. Nat. Commun.8, 1810, (2017).
  13. ↑ Jackson, L. N., Chim, N., Shi, C. & Chaput, J. C. Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. Nucleic Acids Res., (2019).
  14. ↑ Orgel, L. E. A simpler nucleic acid. Science290, 1306-1307, (2000).
  15. ↑ Liu, L. S. et al. alpha-l-Threose Nucleic Acids as Biocompatible Antisense Oligonucleotides for Suppressing Gene Expression in Living Cells. ACS Appl Mater Interfaces10, 9736-9743, (2018).

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