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nucleic acid (TNA) is an artificial genetic polymer in which the natural five-carbon ribose sugar found in RNA has been replaced by an unnatural four-carbon threose sugar.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 it's 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 biopolymers, macromolecules, essential to all known forms of life. 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 version of ribose, the polymer is DNA.

<span class="mw-page-title-main">Nucleotide</span> Biological molecules that form the building blocks of 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.

<span class="mw-page-title-main">Nucleobase</span> Nitrogen-containing biological compounds that form nucleosides

Nucleobases are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. In addition, some viruses have aminoadenine (Z) instead of adenine. It differs in having an extra amine group, creating a more stable bond to thymine.

<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.

<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">Leslie Orgel</span> British chemist

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

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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">Sugar phosphates</span>

Sugar phosphates are often used in biological systems to store or transfer energy. They also form the backbone for DNA and RNA. Sugar phosphate backbone geometry is altered in the vicinity of the modified nucleotides.

<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)

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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.
  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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