1
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Majumdar B, Sarma D, Lee EM, Setterholm NA, Chaput JC. An improved synthesis of guanosine TNA phosphoramidite for oligonucleotide synthesis. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-12. [PMID: 38904107 DOI: 10.1080/15257770.2024.2369688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024]
Abstract
The chemical synthesis of guanosine nucleosides generates both the N9 and N7 regioisomers, which require careful separation to obtain the desired N9 isomer. To preferentially obtain the N9 isomer, a bulky diphenylcarbamoyl (DPC) group can be installed at the O6 position of guanine. However, installation of the DPC group presents a challenging task due to low solubility of the N-acetyl protected guanine. Here we report the usage of commercially available 2-amino-6-chloro purine as a new strategy that offers a more efficient route to the synthesis of the guanine phosphoramidite of threose nucleic acid (TNA).
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Affiliation(s)
- Biju Majumdar
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA
| | - Daisy Sarma
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA
| | - Erica M Lee
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA
| | - Noah A Setterholm
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California, USA
- Department of Chemistry, University of California, Irvine, California, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California, USA
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2
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Barpuzary B, Negria S, Chaput JC. Improved synthesis and polymerase recognition of 7-deaza-7-modified α-l-threofuranosyl guanosine analogs. RSC Adv 2024; 14:19701-19706. [PMID: 38903677 PMCID: PMC11188673 DOI: 10.1039/d4ra03029j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/05/2024] [Indexed: 06/22/2024] Open
Abstract
Threofuranosyl nucleic acid (TNA), an artificial genetic polymer known for its nuclease resistance and acid stability, has grown in popularity as a genetically-encoded material for applications in synthetic biology and biomedicine. TNA oligonucleotide synthesis requires enzymatic or solid phase synthesis pathways that rely on monomer building blocks that are not commercially available and can only be obtained by chemical synthesis. Here we present a synthetic route to 7-deaza-7-modified tGTP and phosphoramidite analogs that is operationally simpler than our previously described strategy. The new methodology offers an HPLC-free route to tGTP analogs that are recognized by engineered TNA polymerases and can be incorporated with continued TNA synthesis.
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Affiliation(s)
- Bhawna Barpuzary
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA
| | - Sergey Negria
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA
- Department of Chemistry, University of California Irvine CA 92697-3958 USA
- Department of Molecular Biology and Biochemistry, University of California CA 92697-3958 USA
- Department of Chemical and Biomolecular Engineering, University of California Irvine CA 92697-3958 USA
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3
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Wang J, Yu H. Threose nucleic acid as a primitive genetic polymer and a contemporary molecular tool. Bioorg Chem 2024; 143:107049. [PMID: 38150936 DOI: 10.1016/j.bioorg.2023.107049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023]
Abstract
Nucleic acids serve a dual role as both genetic materials in living organisms and versatile molecular tools for various applications. Threose nuclei acid (TNA) stands out as a synthetic genetic polymer, holding potential as a primitive genetic material and as a contemporary molecular tool. In this review, we aim to provide an extensive overview of TNA research progress in these two key aspects. We begin with a retrospect of the initial discovery of TNA, followed by an in-depth look at the structural features of TNA duplex and experimental assessment of TNA as a possible RNA progenitor during early evolution of life on Earth. In the subsequent section, we delve into the recent development of TNA molecular tools such as aptamers, catalysts and antisense oligonucleotides. We emphasize the practical application of functional TNA molecules in the realms of targeted protein degradation and selective gene silencing. Our review culminates with a discussion of future research directions and the technical challenges that remain to be addressed in the field of TNA research.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China.
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4
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Shepard SM, Jessen HJ, Cummins CC. Beyond Triphosphates: Reagents and Methods for Chemical Oligophosphorylation. J Am Chem Soc 2022; 144:7517-7530. [PMID: 35471019 DOI: 10.1021/jacs.1c07990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligophosphates play essential roles in biochemistry, and considerable research has been directed toward the synthesis of both naturally occurring oligophosphates and their synthetic analogues. Greater attention has been given to mono-, di-, and triphosphates, as these are present in higher concentrations biologically and easier to synthesize. However, extended oligophosphates have potent biochemical roles, ranging from blood coagulation to HIV drug resistance. Sporadic reports have slowly built a niche body of literature related to the synthesis and study of extended oligophosphates, but newfound interests and developments have the potential to rapidly expand this field. Here we report on current methods to synthesize oligophosphates longer than triphosphates and comment on the most important future directions for this area of research. The state of the art has provided fairly robust methods for synthesizing nucleoside 5'-tetra- and pentaphosphates as well as dinucleoside 5',5'-oligophosphates. Future research should endeavor to push such syntheses to longer oligophosphates while developing synthetic methodologies for rarer morphologies such as 3'-nucleoside oligophosphates, polyphosphates, and phosphonate/thiophosphate analogues of these species.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg & Cluster of Excellence livMatS, FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
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5
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Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:bios12020093. [PMID: 35200353 PMCID: PMC8869748 DOI: 10.3390/bios12020093] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 05/07/2023]
Abstract
Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.
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Affiliation(s)
- Fei Wang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pan Li
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
- Correspondence:
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6
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Li Q, Maola VA, Chim N, Hussain J, Lozoya-Colinas A, Chaput JC. Synthesis and Polymerase Recognition of Threose Nucleic Acid Triphosphates Equipped with Diverse Chemical Functionalities. J Am Chem Soc 2021; 143:17761-17768. [PMID: 34637287 DOI: 10.1021/jacs.1c08649] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Expanding the chemical space of evolvable non-natural genetic polymers (XNAs) to include functional groups that enhance protein target binding affinity offers a promising route to therapeutic aptamers with high biological stability. Here we describe the chemical synthesis and polymerase recognition of 10 chemically diverse functional groups introduced at the C-5 position of α-l-threofuranosyl uridine nucleoside triphosphate (tUTP). We show that the set of tUTP substrates is universally recognized by the laboratory-evolved polymerase Kod-RSGA. Insights into the mechanism of TNA synthesis were obtained from a high-resolution X-ray crystal structure of the postcatalytic complex bound to the primer-template duplex. A structural analysis reveals a large cavity in the enzyme active site that can accommodate the side chain of C-5-modified tUTP substrates. Our findings expand the chemical space of evolvable nucleic acid systems by providing a synthetic route to artificial genetic polymers that are uniformly modified with diversity-enhancing functional groups.
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7
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Abstract
Genomes can be viewed as constantly updated memory systems where information propagated in cells is refined over time by natural selection. This process, commonly known as heredity and evolution, has been the sole domain of DNA since the origin of prokaryotes. Now, some 3.5 billion years later, the pendulum of discovery has swung in a new direction, with carefully trained practitioners enabling the replication and evolution of "xeno-nucleic acids" or "XNAs"-synthetic genetic polymers in which the natural sugar found in DNA and RNA has been replaced with a different type of sugar moiety. XNAs have attracted significant attention as new polymers for synthetic biology, biotechnology, and medicine because of their unique physicochemical properties that may include increased biological stability, enhanced chemical stability, altered helical geometry, or even elevated thermodynamics of Watson-Crick base pairing.This Account describes our contribution to the field of synthetic biology, where chemical synthesis and polymerase engineering have allowed my lab and others to extend the concepts of heredity and evolution to synthetic genetic polymers with backbone structures that are distinct from those found in nature. I will begin with a discussion of α-l-threofuranosyl nucleic acid (TNA), a specific type of XNA that was chosen as a model system to represent any XNA system. I will then proceed to discuss advances in organic chemistry that were made to enable the synthesis of gram quantities of TNA phosphoramidites and nucleoside triphosphates, the monomers used for solid-phase and polymerase-mediated TNA synthesis, respectively. Next, I will recount our development of droplet-based optical sorting (DrOPS), a single-cell microfluidic technique that was established to evolve XNA polymerases in the laboratory. This section will conclude with structural insights that have been gained by solving X-ray crystal structures of a laboratory-evolved TNA polymerase and a natural DNA polymerase that functions with general reverse transcriptase activity on XNA templates.The final passage of this Account will examine the role that XNAs have played in synthetic biology by highlighting examples in which engineered polymerases have enabled the evolution of biologically stable affinity reagents (aptamers) and catalysts (XNAzymes) as well as the storage and retrieval of binary information encoded in electronic word and picture file formats. Because these examples provide only a glimpse of what the future may have in store for XNA, I will conclude the Account with my thoughts on how synthetic genetic polymers could help drive new innovations in synthetic biology and molecular medicine.
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Affiliation(s)
- John C. Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
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8
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Zhang W, Kim SC, Tam CP, Lelyveld VS, Bala S, Chaput JC, Szostak JW. Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization. Nucleic Acids Res 2021; 49:646-656. [PMID: 33347562 PMCID: PMC7826252 DOI: 10.1093/nar/gkaa1215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3'-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.
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Affiliation(s)
- Wen Zhang
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chun Pong Tam
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Victor S Lelyveld
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Saikat Bala
- Department of Chemistry and of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - John C Chaput
- Department of Chemistry and of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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9
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Mei H, Wang Y, Yik EJ, Chaput JC. Synthesis and polymerase recognition of a pyrrolocytidine TNA triphosphate. Biopolymers 2020; 112:e23388. [PMID: 32615644 DOI: 10.1002/bip.23388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 01/03/2023]
Abstract
Synthetic genetics is an area of synthetic biology that aims to extend the properties of heredity and evolution to artificial genetic polymers, commonly known as xeno-nucleic acids or XNAs. In addition to establishing polymerases that are able to convert genetic information back and forth between DNA and XNA, efforts are underway to construct XNAs with expanded chemical functionality. α-L-Threose nucleic acid (TNA), a type of XNA that is recalcitrant to nuclease digestion and amenable to Darwinian evolution, provides a model system for developing XNAs with functional groups that are not present in natural DNA and RNA. Here, we describe the synthesis and polymerase activity of a cytidine TNA triphosphate analog (6-phenyl-pyrrolocytosine, tCp TP) that maintains Watson-Crick base pairing with guanine. Polymerase-mediated primer extension assays show that tCp TP is an efficient substrate for Kod-RI, a DNA-dependent TNA polymerase developed to explore the functional properties of TNA by in vitro selection. Fidelity studies reveal that a cycle of TNA synthesis and reverse transcription occurs with 99.9% overall fidelity when tCp TP and 7-deaza-tGTP are present as TNA substrates. This result expands the toolkit of TNA building blocks available for in vitro selection.
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Affiliation(s)
- Hui Mei
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.,Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, China
| | - Yajun Wang
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Eric J Yik
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - John C Chaput
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
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10
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Liao JY, Bala S, Ngor AK, Yik EJ, Chaput JC. P(V) Reagents for the Scalable Synthesis of Natural and Modified Nucleoside Triphosphates. J Am Chem Soc 2019; 141:13286-13289. [PMID: 31298849 DOI: 10.1021/jacs.9b04728] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural and modified nucleoside triphosphates impact nearly every major aspect of healthcare research from DNA sequencing to drug discovery. However, a scalable synthetic route to these molecules has long been hindered by the need for purification by high performance liquid chromatography (HPLC). Here, we describe a fundamentally different approach that uses a novel P(V) pyrene pyrophosphate reagent to generate derivatives that are purified by silica gel chromatography and converted to the desired compounds on scales vastly exceeding those achievable by HPLC. The power of this approach is demonstrated through the synthesis of a broad range of natural and unnatural nucleoside triphosphates (dNTPs and xNTPs) using protocols that are efficient, inexpensive, and operationally straightforward.
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Affiliation(s)
- Jen-Yu Liao
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - Saikat Bala
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - Arlene K Ngor
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - Eric J Yik
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - John C Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
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11
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Lackey HH, Peterson EM, Chen Z, Harris JM, Heemstra JM. Thermostability Trends of TNA:DNA Duplexes Reveal Strong Purine Dependence. ACS Synth Biol 2019; 8:1144-1152. [PMID: 30964657 DOI: 10.1021/acssynbio.9b00028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of high fidelity polymerases and streamlined synthesis of threose nucleic acid (TNA) triphosphates and phosphoramidites has made TNA accessible as a motif for generating nuclease-resistant high-affinity aptamers, antisense oligos, and synthetic genetic biopolymers. Little is known, however, about the thermostability trends of TNA:DNA duplexes. Here we investigate the thermostability of 14 TNA:DNA duplexes with the goal of elucidating the fundamental factors governing TNA:DNA duplex stability. We find that purine content in TNA significantly influences the stability and conformation of TNA:DNA duplexes. Low TNA purine content destabilizes duplexes, with Tm values often 5 °C lower than analogous DNA:DNA and RNA:DNA duplexes. By contrast, TNA:DNA duplexes having high TNA purine content display greater stability than DNA:DNA or RNA:DNA duplexes having the same sequences. High TNA purine content leads TNA:DNA duplexes to adopt conformations similar to RNA:RNA (A-form) configuration, whereas duplexes with low TNA purine content have conformations more similar to DNA:DNA (B-form) configuration. These insights provide a basis for understanding and predicting TNA:DNA duplex stability, which is anticipated to guide the practical use of TNA in biotechnology applications.
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Affiliation(s)
- Hershel H. Lackey
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric M. Peterson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhe Chen
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Joel M. Harris
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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12
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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13
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Bala S, Liao JY, Zhang L, Tran CN, Chim N, Chaput JC. Synthesis of 2′-Deoxy-α-l-threofuranosyl Nucleoside Triphosphates. J Org Chem 2018; 83:8840-8850. [DOI: 10.1021/acs.joc.8b00875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Saikat Bala
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - Jen-Yu Liao
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - Li Zhang
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - Chantel N. Tran
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - Nicholas Chim
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - John C. Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
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14
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Tasnádi G, Jud W, Hall M, Baldenius K, Ditrich K, Faber K. Evaluation of Natural and Synthetic Phosphate Donors for the Improved Enzymatic Synthesis of Phosphate Monoesters. Adv Synth Catal 2018; 360:2394-2401. [PMID: 30333715 PMCID: PMC6174958 DOI: 10.1002/adsc.201800306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Indexed: 11/18/2022]
Abstract
Undesired product hydrolysis along with large amounts of waste in form of inorganic monophosphate by-product are the main obstacles associated with the use of pyrophosphate in the phosphatase-catalyzed synthesis of phosphate monoesters on large scale. In order to overcome both limitations, we screened a broad range of natural and synthetic organic phosphate donors with several enzymes on a broad variety of hydroxyl-compounds. Among them, acetyl phosphate delivered stable product levels and high phospho-transfer efficiency at the lower functional pH-limit, which translated into excellent productivity. The protocol is generally applicable to acid phosphatases and compatible with a range of diverse substrates. Preparative-scale transformations using acetyl phosphate synthesized from cheap starting materials yielded multiple grams of various sugar phosphates with up to 433 g L-1 h-1 space-time yield and 75% reduction of barium phosphate waste.
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Affiliation(s)
- Gábor Tasnádi
- Austrian Centre of Industrial Biotechnology, c/o
- Department of Chemistry, Organic & Bioorganic Chemistry University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Wolfgang Jud
- Department of Chemistry, Organic & Bioorganic Chemistry University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Mélanie Hall
- Department of Chemistry, Organic & Bioorganic Chemistry University of Graz Heinrichstrasse 28 8010 Graz Austria
| | - Kai Baldenius
- White Biotechnology Research Biocatalysis BASF SE Carl-Bosch-Strasse 38 67056 Ludwigshafen Germany
| | - Klaus Ditrich
- White Biotechnology Research Biocatalysis BASF SE Carl-Bosch-Strasse 38 67056 Ludwigshafen Germany
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry University of Graz Heinrichstrasse 28 8010 Graz Austria
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15
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Mei H, Liao JY, Jimenez RM, Wang Y, Bala S, McCloskey C, Switzer C, Chaput JC. Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues. J Am Chem Soc 2018; 140:5706-5713. [PMID: 29667819 DOI: 10.1021/jacs.7b13031] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection. Unfortunately, the presence of manganese ions in the transcription mixture leads to the misincorporation of tGTP nucleotides opposite dG residues in the templating strand, which are detected as G-to-C transversions when the TNA is reverse transcribed back into DNA. Here we report the synthesis and fidelity of TNA replication using 7-deaza-7-modified guanosine base analogues in the DNA template and incoming TNA nucleoside triphosphate. Our findings reveal that tGTP misincorporation occurs via a Hoogsteen base pair in which the incoming tGTP residue adopts a syn conformation with respect to the sugar. Substitution of tGTP for 7-deaza-7-phenyl tGTP enabled the synthesis of TNA polymers with >99% overall fidelity. A TNA library containing the 7-deaza-7-phenyl guanine analogue was used to evolve a biologically stable TNA aptamer that binds to HIV reverse transcriptase with low nanomolar affinity.
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Affiliation(s)
| | | | | | | | | | | | - Christopher Switzer
- Department of Chemistry , University of California , Riverside , California 92521 , United States
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Mei H, Chaput JC. Expanding the chemical diversity of TNA with tUTP derivatives that are substrates for a TNA polymerase. Chem Commun (Camb) 2018; 54:1237-1240. [PMID: 29340357 DOI: 10.1039/c7cc09130c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Expanding the chemical diversity of threose nucleic acid (TNA) beyond the natural bases would enable the development of TNA polymers with enhanced physicochemical properties. Here, we describe a versatile approach for increasing the chemical diversity of TNA using 5-alkynyl-modified α-l-threofuranosyl uridine triphosphates that are substrates for a TNA polymerase.
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Affiliation(s)
- Hui Mei
- Departments of Pharmaceutical Sciences, Chemistry, Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3958, USA.
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17
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Sau SP, Chaput JC. A Gram-Scale HPLC-Free Synthesis of TNA Triphosphates Using an Iterative Phosphorylation Strategy. Org Lett 2017; 19:4379-4382. [DOI: 10.1021/acs.orglett.7b02099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sujay P. Sau
- Departments of Pharmaceutical
Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
| | - John C. Chaput
- Departments of Pharmaceutical
Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
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