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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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2
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Sierant M, Kulik K, Sochacka E, Szewczyk R, Sobczak M, Nawrot B. Cytochrome c Catalyzes the Hydrogen Peroxide-Assisted Oxidative Desulfuration of 2-Thiouridines in Transfer RNAs. Chembiochem 2018; 19:687-695. [PMID: 29287127 DOI: 10.1002/cbic.201700692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Indexed: 12/14/2022]
Abstract
The 5-substituted 2-thiouridines (R5S2Us) present in the first (wobble) position of the anticodon of transfer RNAs (tRNAs) contribute to accuracy in reading mRNA codons and tuning protein synthesis. Previously, we showed that, under oxidative stress conditions in vitro, R5S2Us were sensitive to hydrogen peroxide (H2 O2 ) and that their oxidative desulfuration produced 5-substituted uridines (R5Us) and 4-pyrimidinone nucleosides (R5H2Us) at a ratio that depended on the pH and an R5 substituent. Here, we demonstrate that the desulfuration of 2-thiouridines, either alone or within an RNA/tRNA chain, is catalyzed by cytochrome c (cyt c). Its kinetics are similar to those of Fenton-type catalytic 2-thiouridine (S2U) desulfuration. Cyt c/H2 O2 - and FeII -mediated reactions deliver predominantly 4-pyrimidinone nucleoside (H2U)-type products. The pathway of the cyt c/H2 O2 -peroxidase-mediated S2U→H2U transformation through uridine sulfenic (U-SOH), sulfinic (U-SO2 H), and sulfonic (U-SO3 H) intermediates is confirmed by LC-MS. The cyt c/H2 O2 -mediated oxidative damage of S2U-tRNA may have biological relevance through alteration of the cellular functions of transfer RNA.
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Affiliation(s)
- Małgorzata Sierant
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Katarzyna Kulik
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz, 90-924, Poland
| | - Rafal Szewczyk
- Department of Industrial Microbiology and Biotechnology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, Lodz, 90-237, Poland
| | - Milena Sobczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, Lodz, 90-363, Poland
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Kaczmarek R, Kaźmierski S, Pawlak T, Radzikowska E, Baraniak J. Assignment of the absolute configuration at stereogenic phosphorus atoms in P-diastereomers of dithymidyl-(N3′→P5′)-phosphoramidothioate. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nawrot B, Michalak O, Mikołajczyk B, Stec WJ. Acyclic analogs of nucleosides based on tris(hydroxymethyl)phosphine oxide: synthesis and incorporation into short DNA oligomers. HETEROCYCL COMMUN 2015. [DOI: 10.1515/hc-2015-0173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AbstractTris-(hydroxymethyl)phosphine oxide (THPO) to a certain extent resembles a part of 2′-deoxyribofuranose, although it exists in an acyclic form only and the oxygen atom at the THPO phosphorus center provides additional hydration site or acceptor of hydrogen bonds. After proper protection of hydroxyl groups, THPO was functionalized with nucleobases and converted into phosphoramidite monomers suitable for incorporation into growing oligonucleotide chains within the solid phase synthesis protocol. The resultant THPO-DNA analogs show reduced affinity to complementary DNA strands, and are resistant towards snake venom and calf spleen exonucleases.
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Affiliation(s)
- Barbara Nawrot
- 1Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Olga Michalak
- 2Pharmaceutical Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland
| | - Barbara Mikołajczyk
- 3Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Wojciech J. Stec
- 3Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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Kwiatkowska A, Sobczak M, Mikolajczyk B, Janczak S, Olejniczak AB, Sochacki M, Lesnikowski ZJ, Nawrot B. siRNAs Modified with Boron Cluster and Their Physicochemical and Biological Characterization. Bioconjug Chem 2013; 24:1017-26. [DOI: 10.1021/bc400059y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Slawomir Janczak
- Laboratory of Molecular Virology
and Biological Chemistry, Institute of Medical Biology of the Polish Academy of Sciences, Lodowa 106, 92-232
Lodz, Poland
| | - Agnieszka B. Olejniczak
- Laboratory of Molecular Virology
and Biological Chemistry, Institute of Medical Biology of the Polish Academy of Sciences, Lodowa 106, 92-232
Lodz, Poland
| | | | - Zbigniew J. Lesnikowski
- Laboratory of Molecular Virology
and Biological Chemistry, Institute of Medical Biology of the Polish Academy of Sciences, Lodowa 106, 92-232
Lodz, Poland
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Krishna H, Caruthers MH. Solid-phase synthesis, thermal denaturation studies, nuclease resistance, and cellular uptake of (oligodeoxyribonucleoside)methylborane phosphine-DNA chimeras. J Am Chem Soc 2011; 133:9844-54. [PMID: 21585202 DOI: 10.1021/ja201314q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The major hurdle associated with utilizing oligodeoxyribonucleotides for therapeutic purposes is their poor delivery into cells coupled with high nuclease susceptibility. In an attempt to combine the nonionic nature and high nuclease stability of the P-C bond of methylphosphonates with the high membrane permeability, low toxicity, and improved gene silencing ability of borane phosphonates, we have focused our research on the relatively unexplored methylborane phosphine (Me-P-BH(3)) modification. This Article describes the automated solid-phase synthesis of mixed-backbone oligodeoxynucleotides (ODNs) consisting of methylborane phosphine and phosphate or thiophosphate linkages (16-mers). Nuclease stability assays show that methylborane phosphine ODNs are highly resistant to 5' and 3' exonucleases. When hybridized to a complementary strand, the ODN:RNA duplex was more stable than its corresponding ODN:DNA duplex. The binding affinity of ODN:RNA duplex increased at lower salt concentration and approached that of a native DNA:RNA duplex under conditions close to physiological saline, indicating that the Me-P-BH(3) linkage is positively charged. Cellular uptake measurements indicate that these ODNs are efficiently taken up by cells even when the strand is 13% modified. Treatment of HeLa cells and WM-239A cells with fluorescently labeled ODNs shows significant cytoplasmic fluorescence when viewed under a microscope. Our results suggest that methylborane phosphine ODNs may prove very valuable as potential candidates in antisense research and RNAi.
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Affiliation(s)
- Heera Krishna
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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Gokhale SS, Gogoi K, Kumar VA. Probing Binding Preferences of DNA and RNA: Backbone Chirality of Thioacetamido-Linked Nucleic Acids and iso-Thioacetamido-Linked Nucleic Acids to Differentiate DNA versus RNA Selective Binding. J Org Chem 2010; 75:7431-4. [DOI: 10.1021/jo1014036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sachin S. Gokhale
- Division Of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Khirud Gogoi
- Division Of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
| | - Vaijayanti A. Kumar
- Division Of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune-411008, India
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Identification of thioaptamer ligand against E-selectin: potential application for inflamed vasculature targeting. PLoS One 2010; 5. [PMID: 20927342 PMCID: PMC2948018 DOI: 10.1371/journal.pone.0013050] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 09/02/2010] [Indexed: 01/16/2023] Open
Abstract
Active targeting of a drug carrier to a specific target site is crucial to provide a safe and efficient delivery of therapeutics and imaging contrast agents. E-selectin expression is induced on the endothelial cell surface of vessels in response to inflammatory stimuli but is absent in the normal vessels. Thus, E-selectin is an attractive molecular target, and high affinity ligands for E-selectin could be powerful tools for the delivery of therapeutics and/or imaging agents to inflamed vessels. In this study, we identified a thiophosphate modified aptamer (thioaptamer, TA) against E-selectin (ESTA-1) by employing a two-step selection strategy: a recombinant protein-based TA binding selection from a combinatorial library followed by a cell-based TA binding selection using E-selectin expressing human microvascular endothelial cells. ESTA-1 selectively bound to E-selectin with nanomolar binding affinity (KD = 47 nM) while exhibiting minimal cross reactivity to P- and L-selectin. Furthermore, ESTA-1 binding to E-selectin on the endothelial cells markedly antagonized the adhesion (over 75% inhibition) of sLex positive HL-60 cells at nanomolar concentration. ESTA-1 also bound specifically to the inflamed tumor-associated vasculature of human carcinomas derived from breast, ovarian, and skin but not to normal organs, and this binding was highly associated with the E-selectin expression level. Similarly, intravenously injected ESTA-1 demonstrated distinct binding to the tumor vasculature in a breast cancer xenograft model. Together, our data substantiates the discovery of a thioaptamer (ESTA-1) that binds to E-selectin with high affinity and specificity, thereby highlighting the potential application of ESTA-1 for E-selectin targeted delivery.
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Padié C, Maszewska M, Majchrzak K, Nawrot B, Caminade AM, Majoral JP. Polycationic phosphorus dendrimers: synthesis, characterization, study of cytotoxicity, complexation of DNA, and transfection experiments. NEW J CHEM 2009. [DOI: 10.1039/b815259d] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gogoi K, Gunjal AD, Phalgune UD, Kumar VA. Synthesis and RNA binding selectivity of oligonucleotides modified with five-atom thioacetamido nucleic acid backbone structures. Org Lett 2007; 9:2697-700. [PMID: 17552532 DOI: 10.1021/ol070990u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Convenient chemical synthesis and incorporation of dithymidine and thymidine-cytidine dimer blocks connected with a five-atom amide linker N3'-CO-CH2-S-CH2 into oligonucleotides (ONs) are reported. The UV-Tm experiments for binding affinities of these mixed backbone ONs with complementary DNA and RNA sequences revealed important results such as significantly higher RNA-binding selectivity as compared with complementary DNA. NMR studies of the dimer blocks suggested a marginal increase in the N-type sugar conformations over that of the native DNA.
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Affiliation(s)
- Khirud Gogoi
- Division of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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Nawrot B, Sobczak M, Wójcik M, Janicka M, Nowak M, Cypryk M, Stec WJ. A novel class of DNA analogs bearing 5'-C-phosphonothymidine units: synthesis and physicochemical and biochemical properties. Oligonucleotides 2006; 16:68-82. [PMID: 16584296 DOI: 10.1089/oli.2006.16.68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
S(C) and R(C) diastereomers of 5'-C-(O,O-diethyl)-phosphonylthymidine ((R)T and (S)T) were used for the synthesis of the dimers T(R)T and T(S)T, respectively. These dimers were incorporated at selected sites in oligonucleotide constructs. Melting temperature (Tm) experiments demonstrated that relative to the unmodified oligodeoxyribonucleotide, the presence of the (R)T moiety reduced the thermal stability of the duplexes by approximately 5.0 degrees C per modification, whereas their (S)T counterparts only slightly destabilized the duplex structure (deltaTm < or = 1 degree C/modification). The stability of the triple-helical complexes containing one, two, or three modified thymidines is slightly higher than that of the parent complex. Nuclease resistance studies performed with snake venom phosphodiesterase, calf spleen phosphodiesterase, and 3'-exonuclease from human plasma showed that cleavage of the oligonucleotides at the site of the modification was completely suppressed regardless of the stereochemistry of the 5'-C-chiral center. The influence of the (R)T and (S)T modification in the recognition sequence of HindIII, EcoRI, and HpaI restriction endonucleases was also investigated. Although the catalytic activity of HindIII was not affected by the presence of the 5'-C-ethoxyphosphonyl modification, the activities of the two remaining restriction enzymes were partially suppressed depending on the site of modification or the stereochemistry of the modification or both ((R)T vs. (S)T).
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Affiliation(s)
- Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies of Polish Academy of Sciences, 90-363 Lodz, Poland.
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Seregin KV, Chudinov MV, Iurkevich AM, Shvets VI. An efficient synthesis of 3′-amino-3′-deoxythymidine derivatives. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2005; 31:147-50. [PMID: 15889788 DOI: 10.1007/s11171-005-0018-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
An efficient method of reduction of 3'-azido-3'-deoxythymidine and its 5'-protected derivatives to 3'-aminothymidine derivatives on a palladium catalyst using ammonium formate as a source of hydrogen was suggested.
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13
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Olejniczak S, Sobczak M, Potrzebowski MJ, Polak M, Plavec J, Nawrot B. Assignment of absolute configuration at phosphorus of P-chiral diastereomers of deoxyribonucleoside methanephosphonamidates by means of NMR spectroscopy. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.03.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Nawrot B, Sobczak M, Antoszczyk S. Synthesis of dinucleoside (N3'-->MeP5') methanephosphonamidates. Org Lett 2002; 4:1799-802. [PMID: 12000302 DOI: 10.1021/ol0259084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] Three different approaches were used for the synthesis of dinucleoside methanephosphonamidates [3'-NH-P(O)(CH3)O-5'], starting from dichloromethylphosphine or dichloromethanephosphonate as the phosphorus-containing moiety. 5'-DMT-3'-amino-3'-deoxythymidine and N(4)-benzoyl-5'-DMT-3'-amino-2',3'-dideoxycytidine were used as the aminonucleoside precursors and the respective 3'-protected nucleosides (thymidine or N(4)-benzoyl-2'-deoxycytidine) as the 5'-hydroxyl reagents.
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Affiliation(s)
- Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
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