Threose nucleic acid information

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nucleic acid (TNA) is an artificial genetic polymer in which the natural five-carbon ribose sugar found in RNA has been replaced by an unnatural four-carbon threose sugar.^[1] Invented by Albert Eschenmoser as part of his quest to explore the chemical etiology of RNA,^[2] TNA has become an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]

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]

^ ^a ^b Schöning, K. U. et al. Chemical etiology of nucleic acid structure: the a-threofuranosyl-(3'-->2') oligonucleotide system. Science 290, 1347-1351, (2000)
^ Eschenmoser, A. Chemical etiology of nucleic acid structure. Science 284, 2118-2124, (1999).
^ 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.
^ Culbertson, M. C. et al. Evaluating TNA stability under simulated physiological conditions. Bioorg. Med. Chem. Lett. 26, 2418-2421, (2016).
^ 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).
^ Larsen, A. C. et al. A general strategy for expanding polymerase function by droplet microfluidics. Nat. Commun. 7, 11235, (2016).
^ 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).
^ 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).
^ 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).
^ 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).
^ Pinheiro, V. B. et al. Synthetic genetic polymers capable of heredity and evolution. Science 336, 341-344, (2012).
^ 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).
^ 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).

[:0-1] Schöning, K. U. et al. Chemical etiology of nucleic acid structure: the a-threofuranosyl-(3'-->2') oligonucleotide system. Science 290, 1347-1351, (2000)

[2] Eschenmoser, A. Chemical etiology of nucleic acid structure. Science 284, 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).

[:1-8] 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. Science 336, 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).

Threose nucleic acid information

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