1
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Novikova D, Sagaidak A, Vorona S, Tribulovich V. A Visual Compendium of Principal Modifications within the Nucleic Acid Sugar Phosphate Backbone. Molecules 2024; 29:3025. [PMID: 38998973 PMCID: PMC11243533 DOI: 10.3390/molecules29133025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of redesigned natural nucleic acids have been proposed in recent years, the vast majority of them are combinations of simple modifications proposed over the past 50 years. This review is devoted to the main modifications of the sugar phosphate backbone of natural nucleic acids known to date. Here, we propose a systematization of existing knowledge about modifications of nucleic acid monomers and an acceptable classification from the point of view of chemical logic. The visual representation is intended to inspire researchers to create a new type of modification or an original combination of known modifications that will produce unique oligonucleotides with valuable characteristics.
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Affiliation(s)
- Daria Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Aleksandra Sagaidak
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Svetlana Vorona
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Vyacheslav Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
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2
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Li Q, Trajkovski M, Fan C, Chen J, Zhou Y, Lu K, Li H, Su X, Xi Z, Plavec J, Zhou C. 4'-SCF 3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA. Angew Chem Int Ed Engl 2022; 61:e202201848. [PMID: 36163470 PMCID: PMC9828712 DOI: 10.1002/anie.202201848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Indexed: 01/12/2023]
Abstract
Fluorinated nucleotides are invaluable for 19 F NMR studies of nucleic acid structure and function. Here, we synthesized 4'-SCF3 -thymidine (T 4 ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ ) and incorporated it into DNA by means of solid-phase DNA synthesis. NMR studies showed that the 4'-SCF3 group exhibited a flexible orientation in the minor groove of DNA duplexes and was well accommodated by various higher order DNA structures. The three magnetically equivalent fluorine atoms in 4'-SCF3 -DNA constitute an isolated spin system, offering high 19 F NMR sensitivity and excellent resolution of the positioning of T 4 ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T 4 ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ make it a valuable 19 F NMR probe for quantitatively distinguishing diverse DNA structures with single-nucleotide resolution and for monitoring the dynamics of interactions in the minor groove of double-stranded DNA.
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Affiliation(s)
- Qiang Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China,Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
| | - Marko Trajkovski
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
| | - Chaochao Fan
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Jialiang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Kuan Lu
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Hongjun Li
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
| | - Chuanzheng Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical BiologyCollege of ChemistryNankai UniversityTianjin300071China
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3
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Osawa T, Yano N, Aoyama H, Obika S. Synthesis, Duplex-Forming Ability, and Nuclease Resistance of Oligonucleotides Containing a Thymidine Derivative with a 1-Oxaspiro[4.5]decane Skeleton. Chem Pharm Bull (Tokyo) 2022; 70:699-706. [PMID: 36184452 DOI: 10.1248/cpb.c22-00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chemically modified nucleic acids are essential for the therapeutic application of oligonucleotides. In this study, 6'-C-spiro-thymidine exhibiting a fixed torsion angle γ was designed, synthesized, and incorporated into oligonucleotides. The conformational analysis of the 6'-C-spiro-thymidine monomer revealed that its torsion angle γ was in the +synclinal range (approx. 60°), which is similar to that in a natural RNA duplex, as expected. On the other hand, the sugar conformation of the RNA duplex is known to be predominantly an N-type, whereas that of the synthesized monomer was an S-type. The results of the UV melting analysis demonstrated that the duplex-forming ability of 6'-C-spiro-thymidine was inferior to that of natural DNA. Contrarily, 6'-C-spiro-thymidine could enhance the stability of oligonucleotides toward nucleases. Particularly, the incorporation of 6'-C-spiro-thymidine on the 3'-ends of the oligonucleotides significantly increased the nuclease resistance of the oligonucleotides.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Natsumi Yano
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University
- National Institutes of Biomedical Innovation, Health and Nutrition
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4
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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5
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Živković ML, Gajarský M, Beková K, Stadlbauer P, Vicherek L, Petrová M, Fiala R, Rosenberg I, Šponer J, Plavec J, Trantírek L. Insight into formation propensity of pseudocircular DNA G-hairpins. Nucleic Acids Res 2021; 49:2317-2332. [PMID: 33524154 PMCID: PMC7913771 DOI: 10.1093/nar/gkab029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
We recently showed that Saccharomyces cerevisiae telomeric DNA can fold into an unprecedented pseudocircular G-hairpin (PGH) structure. However, the formation of PGHs in the context of extended sequences, which is a prerequisite for their function in vivo and their applications in biotechnology, has not been elucidated. Here, we show that despite its ‘circular’ nature, PGHs tolerate single-stranded (ss) protrusions. High-resolution NMR structure of a novel member of PGH family reveals the atomistic details on a junction between ssDNA and PGH unit. Identification of new sequences capable of folding into one of the two forms of PGH helped in defining minimal sequence requirements for their formation. Our time-resolved NMR data indicate a possibility that PGHs fold via a complex kinetic partitioning mechanism and suggests the existence of K+ ion-dependent PGH folding intermediates. The data not only provide an explanation of cation-type-dependent formation of PGHs, but also explain the unusually large hysteresis between PGH melting and annealing noted in our previous study. Our findings have important implications for DNA biology and nanotechnology. Overrepresentation of sequences able to form PGHs in the evolutionary-conserved regions of the human genome implies their functionally important biological role(s).
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Affiliation(s)
- Martina Lenarčič Živković
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,Slovenian NMR Centre, National Institute of Chemistry, Ljubljana SI-1000, Slovenia
| | - Martin Gajarský
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Kateřina Beková
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Lukáš Vicherek
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Šponer
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana SI-1000, Slovenia.,EN-FIST Centre of Excellence, Ljubljana SI-1001, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
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6
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Osawa T, Kawaguchi M, Jang YJ, Ito Y, Hari Y. Synthesis and properties of oligonucleotides bearing thymidine derivatives with 1,6-dioxaspiro[4.5]decane skeleton. Bioorg Med Chem 2021; 31:115966. [DOI: 10.1016/j.bmc.2020.115966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 11/29/2022]
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7
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8
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Harp JM, Guenther DC, Bisbe A, Perkins L, Matsuda S, Bommineni GR, Zlatev I, Foster DJ, Taneja N, Charisse K, Maier MA, Rajeev KG, Manoharan M, Egli M. Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity. Nucleic Acids Res 2019; 46:8090-8104. [PMID: 30107495 PMCID: PMC6144868 DOI: 10.1093/nar/gky703] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
Chemical modification is a prerequisite of oligonucleotide therapeutics for improved metabolic stability, uptake and activity, irrespective of their mode of action, i.e. antisense, RNAi or aptamer. Phosphate moiety and ribose C2′/O2′ atoms are the most common sites for modification. Compared to 2′-O-substituents, ribose 4′-C-substituents lie in proximity of both the 3′- and 5′-adjacent phosphates. To investigate potentially beneficial effects on nuclease resistance we combined 2′-F and 2′-OMe with 4′-Cα- and 4′-Cβ-OMe, and 2′-F with 4′-Cα-methyl modification. The α- and β-epimers of 4′-C-OMe-uridine and the α-epimer of 4′-C-Me-uridine monomers were synthesized and incorporated into siRNAs. The 4′α-epimers affect thermal stability only minimally and show increased nuclease stability irrespective of the 2′-substituent (H, F, OMe). The 4′β-epimers are strongly destabilizing, but afford complete resistance against an exonuclease with the phosphate or phosphorothioate backbones. Crystal structures of RNA octamers containing 2′-F,4′-Cα-OMe-U, 2′-F,4′-Cβ-OMe-U, 2′-OMe,4′-Cα-OMe-U, 2′-OMe,4′-Cβ-OMe-U or 2′-F,4′-Cα-Me-U help rationalize these observations and point to steric and electrostatic origins of the unprecedented nuclease resistance seen with the chain-inverted 4′β-U epimer. We used structural models of human Argonaute 2 in complex with guide siRNA featuring 2′-F,4′-Cα-OMe-U or 2′-F,4′-Cβ-OMe-U at various sites in the seed region to interpret in vitro activities of siRNAs with the corresponding 2′-/4′-C-modifications.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Dale C Guenther
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Lydia Perkins
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Donald J Foster
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Nate Taneja
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | - Martin A Maier
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
| | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
- To whom correspondence should be addressed. Tel: +1 615 343 8070; Fax: +1 615 343 0704; . Correspondence may also be addressed to Muthiah Manoharan. Tel: +1 617 551 8319; Fax: +1 617 551 8101;
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
- To whom correspondence should be addressed. Tel: +1 615 343 8070; Fax: +1 615 343 0704; . Correspondence may also be addressed to Muthiah Manoharan. Tel: +1 617 551 8319; Fax: +1 617 551 8101;
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9
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Malek-Adamian E, Fakhoury J, Arnold AE, Martínez-Montero S, Shoichet MS, Damha MJ. Effect of Sugar 2',4'-Modifications on Gene Silencing Activity of siRNA Duplexes. Nucleic Acid Ther 2019; 29:187-194. [PMID: 31084536 PMCID: PMC6686699 DOI: 10.1089/nat.2019.0792] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In this study, we explore the effect of a library of 2′-, 4′-, and 2′,4′-modified uridine nucleosides and their impact on silencing firefly luciferase and on down-regulated in renal cell carcinoma (DRR) gene targets. The modifications studied were 2′-F-ribose, 2′-F-arabinose, 2′-OMe-ribose, 2′-F,4′-OMe-ribose, 2′-F,4′-OMe-arabinose, and 2′-OMe,4′-F-ribose. We found that 2′,4′-modifications are well tolerated within A-form RNA duplexes, leading to virtually no change in melting temperature as assessed by UV thermal melting. The impact of the dual (2′,4′) modification was assessed by comparing gene silencing ability to 2′- or 4′- (singly) modified siRNA counterparts. siRNAs with (2′,4′)-modified overhangs generally outperformed the native siRNA as well as siRNAs with a 2′- or 4′-modified overhang, suggesting that 2′,4′-modified nucleotides interact favorably with Argonaute protein's PAZ domain. Among the most active siRNAs were those with 2′-F,4′-OMe-ribose or 2′-F,4′-OMe-arabinose at the overhangs. When modifications were placed at both overhangs and internal positions, a duplex with the 2′-F (internal) and 2′-F,4′-OMe (overhang) combination was found to be the most potent, followed by the duplex with 2′-OMe (internal) and 2′,4′-diOMe (overhang) modifications. Given the nuclease resistance exhibited by 2′,4′-modified siRNAs, particularly when the modification is placed at or near the overhangs, these findings may allow the creation of superior siRNAs for therapy.
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Affiliation(s)
| | - Johans Fakhoury
- 1Department of Chemistry, McGill University, Montreal, Canada
| | - Amy E Arnold
- 2Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | | | - Molly S Shoichet
- 2Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.,3Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada.,4Department of Chemistry, University of Toronto, Toronto, Canada
| | - Masad J Damha
- 1Department of Chemistry, McGill University, Montreal, Canada
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10
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He XY, Wang J, Lu DD, Wang SQ. Synthesis and Antisense Properties of 2'β-F-Arabinouridine Modified Oligonucleotides with 4'- C-OMe Substituent. Molecules 2018; 23:molecules23092374. [PMID: 30227644 PMCID: PMC6225415 DOI: 10.3390/molecules23092374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 11/16/2022] Open
Abstract
A novel 2′-F,4′-C-OMe–arabinouridine (araU) was successfully synthesized and introduced into oligonucleotides. The oligonucleotide containing 2′-F,4′-C-OMe–araU exhibited improved nuclease resistance and RNA hybridizing selective ability relative to 2′-F–araU. In particular, when 2′-F,4′-C-OMe–araU inserted into C–H⋯F–C bonding-favorable 5′–uridine–purine–3′ steps, the modified oligonucleotide showed remarkable binding affinity and selectivity to RNA complements. Thus, 2′-F,4′-C-OMe–araU has valuable antisense properties and can be used as novel chemical modification for antisense therapeutic strategy.
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Affiliation(s)
- Xiao-Yang He
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Jing Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Dan-Dan Lu
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Sheng-Qi Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
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11
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Malek-Adamian E, Patrascu MB, Jana SK, Martínez-Montero S, Moitessier N, Damha MJ. Adjusting the Structure of 2'-Modified Nucleosides and Oligonucleotides via C4'-α-F or C4'-α-OMe Substitution: Synthesis and Conformational Analysis. J Org Chem 2018; 83:9839-9849. [PMID: 29963864 DOI: 10.1021/acs.joc.8b01329] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the first syntheses of three nucleoside analogues, namely, 2',4'-diOMe-rU, 2'-OMe,4'-F-rU, and 2'-F,4'-OMe-araU, via stereoselective introduction of fluorine or methoxy functionalities at the C4'-α-position of a 4',5'-olefinic intermediate. Conformational analyses of these nucleosides and comparison to other previously reported 2',4'-disubstituted nucleoside analogues make it possible to evaluate the effect of fluorine and methoxy substitution on the sugar pucker, as assessed by NMR, X-ray diffraction, and computational methods. We found that C4'-α-F/OMe substituents reinforce the C3'-endo ( north) conformation of 2'-OMe-rU. Furthermore, the predominant C2'-endo ( south/ east) conformation of 2'-F-araU switches to C3'-endo upon introduction of these substituents at C4'. The nucleoside analogues were incorporated into DNA and RNA oligonucleotides via standard phosphoramidite chemistry, and their effects on the thermal stability of homo- and heteroduplexes were assessed via UV thermal melting experiments. We found that 4'-substituents can modulate the binding affinity of the parent 2'-modified oligomers, inducing a mildly destabilizing or stabilizing effect depending on the duplex type. This study expands the spectrum of oligonucleotide modifications available for rational design of oligonucleotide therapeutics.
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Affiliation(s)
- Elise Malek-Adamian
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Mihai Burai Patrascu
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Sunit Kumar Jana
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Saúl Martínez-Montero
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
| | - Masad J Damha
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec , Canada H3A 0B8
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12
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Páv O, Barvík I, Liboska R, Petrová M, Šimák O, Rosenbergová Š, Novák P, Buděšínský M, Rosenberg I. Tuning the hybridization properties of modified oligonucleotides: from flexible to conformationally constrained phosphonate internucleotide linkages. Org Biomol Chem 2018; 15:701-707. [PMID: 27995239 DOI: 10.1039/c6ob02571d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The concept of conformational restriction leading to the preorganization of modified strands has proven to be successful and has afforded nucleic acid analogues with many interesting properties suitable for various biochemical applications. We utilized this concept to prepare a set of constrained oligonucleotides derived from 1,4-dioxane and 1,3-dioxolane-locked nucleoside phosphonates and evaluated their hybridization affinities towards their complementary RNA strands. With an increase of ΔTm per modification up to +5.2 °C, the hybridization experiments revealed the (S)-2',3'-O-phosphonomethylidene internucleotide linkage as one of the most Tm-increasing modifications reported to date. Moreover, we introduced a novel prediction tool for the pre-selection of potentially interesting chemical modifications of oligonucleotides.
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Affiliation(s)
- Ondřej Páv
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ivan Barvík
- Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116 Prague, Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic. and Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Technická 5, 16628 Prague, Czech Republic
| | - Šárka Rosenbergová
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Pavel Novák
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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13
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Suthagar K, Jiao W, Munier-Lehmann H, Fairbanks AJ. Synthesis of sulfamide analogues of deoxthymidine monophosphate as potential inhibitors of mycobacterial cell wall biosynthesis. Carbohydr Res 2018; 457:32-40. [PMID: 29348046 DOI: 10.1016/j.carres.2018.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/08/2018] [Accepted: 01/08/2018] [Indexed: 11/26/2022]
Abstract
The recently discovered enzyme Mycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt), which catalyses the phosphorylation of deoxythymidine monophosphate (dTMP) to give deoxythymidine diphosphate (dTDP), is indispensable for the growth and survival of M. tuberculosis as it plays an essential role in DNA synthesis. Inhibition of TMPKmt is an attractive avenue for the development of novel anti-tuberculosis agents. Based on the premise that sulfamide may be a suitable isostere of phosphate, deoxythymidine analogues comprising various substituted sulfamides at C5' were modelled in silico into the active site of TMPKmt (PDB accession code: 1N5K) using induced-fit docking methods. A selection of modelled compounds was synthesized, and their activity as inhibitors of TMPKmt was evaluated. Three compounds showed competitive inhibition of TMPKmt in the micromolar range (10-50 μM). Compounds were tested in vitro for anti-mycobacterial activity against M. smegmatis: three compounds showed weak anti-mycobacterial activity (MIC 250 μg/mL).
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Affiliation(s)
- Kajitha Suthagar
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Wanting Jiao
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand; Ferrier Research Institute, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, 28 rue du Dr Roux, 75724, Paris Cedex 15, France; CNRS UMR3523, 28 rue du Dr Roux, France
| | - Antony J Fairbanks
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand; Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
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14
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Malek-Adamian E, Guenther DC, Matsuda S, Martínez-Montero S, Zlatev I, Harp J, Burai Patrascu M, Foster DJ, Fakhoury J, Perkins L, Moitessier N, Manoharan RM, Taneja N, Bisbe A, Charisse K, Maier M, Rajeev KG, Egli M, Manoharan M, Damha MJ. 4'-C-Methoxy-2'-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing. J Am Chem Soc 2017; 139:14542-14555. [PMID: 28937776 DOI: 10.1021/jacs.7b07582] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We designed novel 4'-modified 2'-deoxy-2'-fluorouridine (2'-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4'-C-methoxy (4'-OMe) as the alpha (C4'α) or beta (C4'β) epimers. The C4'α epimer was synthesized by a stereoselective route in six steps; however, both α and β epimers could be obtained by a nonstereoselective approach starting from 2'-F U. 1H NMR analysis and computational investigation of the α-epimer revealed that the 4'-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-epimer led to significant destabilization. Both 4'-OMe epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4'-OMe substituent and the vicinal 5'- and 3'-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs containing several C4'α-epimer monomers in the sense or antisense strands triggered RNAi-mediated gene silencing with efficiencies comparable to that of 2'-F U.
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Affiliation(s)
- Elise Malek-Adamian
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Dale C Guenther
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Shigeo Matsuda
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Saúl Martínez-Montero
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Joel Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Mihai Burai Patrascu
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Donald J Foster
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Johans Fakhoury
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Lydia Perkins
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nicolas Moitessier
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nate Taneja
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | | | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Masad J Damha
- Department of Chemistry, McGill University , 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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15
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Fukal J, Páv O, Buděšínský M, Šebera J, Sychrovský V. The benchmark of 31P NMR parameters in phosphate: a case study on structurally constrained and flexible phosphate. Phys Chem Chem Phys 2017; 19:31830-31841. [DOI: 10.1039/c7cp06969c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A benchmark for structural interpretation of the 31P NMR shift and the 2JP,C spin–spin coupling in the phosphate group was obtained by means of theoretical calculations and measurements in diethylphosphate and 5,5-dimethyl-2-hydroxy-1,3,2-dioxaphosphinane 2-oxide.
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Affiliation(s)
- Jiří Fukal
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Department of Electrotechnology
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16
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Petrová M, Rosenberg I. Synthesis of 4'-Methoxy 2'-Deoxynucleoside Phosphoramidites for Incorporation into Oligonucleotides. ACTA ACUST UNITED AC 2016; 66:1.38.1-1.38.27. [PMID: 27584701 DOI: 10.1002/cpnc.15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This unit contains detailed synthetic protocols for the preparation of 4'-methoxy 2'-deoxynucleoside phosphoramidite monomers for A, G, C, T, and U. First, 3'-silyl-protected 2'-deoxynucleosides (dNs) are converted in two steps to 4',5'-enol acetates as the key starting compounds. Next, 4'-methoxy dNs are prepared by a one-pot procedure comprising N-iodosuccinimide-promoted methoxylation, hydrolysis, and reduction of the formed intermediates. Finally, 3'-phosphoramidites of 4'-methoxy dNs are obtained by a routine three-step procedure. Title phosphoramidite monomers are suitable for the synthesis of oligonucleotides on solid phase according to conventional amidite chemistry. 4'-Methoxy substitution represents a simple modification of the sugar part of dNs, where β-D-erythro epimers preferentially adopt N-type (C3'-endo, RNA-like) conformation. Moreover, it imparts superior chemical stability, nuclease resistance, and excellent hybridization properties to modified 4'-methoxyoligodeoxynucleotides. The strong tendency toward RNA-selective hybridization suggests its potential utilization in antisense and/or RNAi technologies. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Magdalena Petrová
- Department of Bioorganic and Medicinal Chemistry, The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ivan Rosenberg
- Department of Bioorganic and Medicinal Chemistry, The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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17
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Kel'in AV, Zlatev I, Harp J, Jayaraman M, Bisbe A, O'Shea J, Taneja N, Manoharan RM, Khan S, Charisse K, Maier MA, Egli M, Rajeev KG, Manoharan M. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. J Org Chem 2016; 81:2261-79. [PMID: 26940174 DOI: 10.1021/acs.joc.5b02375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although judicious use of chemical modifications has contributed to the success of nucleic acid therapeutics, poor systemic stability remains a major hurdle. The introduction of functional groups around the phosphate backbone can enhance the nuclease resistance of oligonucleotides (ONs). Here, we report the synthesis of enantiomerically pure (R)- and (S)-5'-C-methyl (C5'-Me) substituted nucleosides and their incorporation into ONs. These modifications generally resulted in a decrease in thermal stability of oligonucleotide (ON) duplexes in a manner dependent on the stereoconfiguration at C5' with greater destabilization characteristic of (R)-epimers. Enhanced stability against snake venom phosphodiesterase resulted from modification of the 3'-end of an ON with either (R)- or (S)-C5'-Me nucleotides. The (S)-isomers with different 2'-substituents provided greater resistance against 3'-exonucleases than the corresponding (R)-isomers. Crystal structure analyses of RNA octamers with (R)- or (S)-5'-C-methyl-2'-deoxy-2'-fluorouridine [(R)- or (S)-C5'-Me-2'-FU, respectively] revealed that the stereochemical orientation of the C5'-Me and the steric effects that emanate from the alkyl substitution are the dominant determinants of thermal stability and are likely molecular origins of resistance against nucleases. X-ray and NMR structural analyses showed that the (S)-C5'-Me epimers are spatially and structurally more similar to their natural 5' nonmethylated counterparts than the corresponding (R)-epimers.
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Affiliation(s)
- Alexander V Kel'in
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ivan Zlatev
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Joel Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | - Muthusamy Jayaraman
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Anna Bisbe
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Jonathan O'Shea
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Nate Taneja
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Rajar M Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Saeed Khan
- Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
| | - Klaus Charisse
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin A Maier
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine , Nashville, Tennessee 37232, United States
| | | | - Muthiah Manoharan
- Alnylam Pharmaceuticals , 300 Third Street, Cambridge, Massachusetts 02142, United States
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18
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Hari Y, Obika S. Synthesis and Properties of 2’,4’-Bridged Nucleic Acids Containing Multiple Heteroatoms in the Bridges. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
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19
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Petrová M, Páv O, Buděšínský M, Zborníková E, Novák P, Rosenbergová Š, Pačes O, Liboska R, Dvořáková I, Šimák O, Rosenberg I. Straightforward Synthesis of Purine 4'-Alkoxy-2'-deoxynucleosides: First Report of Mixed Purine-Pyrimidine 4'-Alkoxyoligodeoxynucleotides as New RNA Mimics. Org Lett 2015; 17:3426-9. [PMID: 26133076 DOI: 10.1021/acs.orglett.5b01430] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Purine and pyrimidine 4'-alkoxy-2'-deoxynucleosides were efficiently prepared from nucleoside 4'-5'-enol acetates in three steps by N-iodosuccinimide promoted alkoxylation, hydrolysis, and reduction followed by conversion to phosphoramidite monomers for the solid-phase synthesis of the oligonucleotides. Fully modified 4'-alkoxyoligodeoxynucleotides, which are characterized by a prevalent N-type (RNA-like) conformation, exhibited superior chemical and nuclease resistance as well as excellent hybridization properties with a strong tendency for RNA-selective hybridization, suggesting a potential application of 4'-alkoxy-oligodeoxynucleotides in antisense technologies.
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Affiliation(s)
- Magdalena Petrová
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Ondřej Páv
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Miloš Buděšínský
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Eva Zborníková
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Pavel Novák
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Šárka Rosenbergová
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Ondřej Pačes
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Radek Liboska
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Ivana Dvořáková
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Ondřej Šimák
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Ivan Rosenberg
- Department of Bioorganic and Medicinal Chemistry, Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
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20
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Šipova H, Špringer T, Rejman D, Šimak O, Petrová M, Novák P, Rosenbergová Š, Páv O, Liboska R, Barvík I, Štěpanek J, Rosenberg I, Homola J. 5'-O-Methylphosphonate nucleic acids--new modified DNAs that increase the Escherichia coli RNase H cleavage rate of hybrid duplexes. Nucleic Acids Res 2014; 42:5378-89. [PMID: 24523351 PMCID: PMC4005664 DOI: 10.1093/nar/gku125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Several oligothymidylates containing various ratios of phosphodiester and isopolar 5'-hydroxyphosphonate, 5'-O-methylphosphonate and 3'-O-methylphosphonate internucleotide linkages were examined with respect to their hybridization properties with oligoriboadenylates and their ability to induce RNA cleavage by ribonuclease H (RNase H). The results demonstrated that the increasing number of 5'-hydroxyphosphonate or 5'-O-methylphosphonate units in antisense oligonucleotides (AOs) significantly stabilizes the heteroduplexes, whereas 3'-O-methylphosphonate AOs cause strong destabilization of the heteroduplexes. Only the heteroduplexes with 5'-O-methylphosphonate units in the antisense strand exhibited a significant increase in Escherichia coli RNase H cleavage activity by up to 3-fold (depending on the ratio of phosphodiester and phosphonate linkages) in comparison with the natural heteroduplex. A similar increase in RNase H cleavage activity was also observed for heteroduplexes composed of miRNA191 and complementary AOs containing 5'-O-methylphosphonate units. We propose for this type of AOs, working via the RNase H mechanism, the abbreviation MEPNA (MEthylPhosphonate Nucleic Acid).
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Affiliation(s)
- Hana Šipova
- Institute of Photonics and Electronics AS CR, v.v.i., Chaberská 57, 182 51 Prague, Czech Republic, Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2., 166 10 Prague, Czech Republic and Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague, Czech Republic
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21
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Kratochvílová I, Vala M, Weiter M, Špérová M, Schneider B, Páv O, Šebera J, Rosenberg I, Sychrovský V. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: Complex theoretical and experimental studies. Biophys Chem 2013; 180-181:127-34. [DOI: 10.1016/j.bpc.2013.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/19/2013] [Accepted: 07/20/2013] [Indexed: 12/31/2022]
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22
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Hari Y, Morikawa T, Osawa T, Obika S. Synthesis and properties of 2'-O,4'-C-ethyleneoxy bridged 5-methyluridine. Org Lett 2013; 15:3702-5. [PMID: 23815244 DOI: 10.1021/ol401566r] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
2'-O,4'-C-Ethyleneoxy bridged 5-methyluridine (EoNA-T), possessing a seven-membered linkage and an anomeric 4'-carbon, was synthesized and introduced into oligonucleotides by using an automated DNA synthesizer. The EoNA-modified oligonucleotides significantly stabilized the duplexes with single-stranded RNA and triplexes with double-stranded DNA relative to the natural oligonucleotide and oligonucleotides modified by another seven-membered bridged 5-methyluridine, 2',4'-BNA(COC)-T. In addition, EoNA-T showed excellent nuclease resistance.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan.
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23
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Hari Y, Osawa T, Obika S. Synthesis and duplex-forming ability of oligonucleotides containing 4'-carboxythymidine analogs. Org Biomol Chem 2012; 10:9639-49. [PMID: 23138991 DOI: 10.1039/c2ob26712h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oligonucleotides containing 4'-carboxy-, 4'-methoxycarbonyl-, 4'-carbamoyl-, and 4'-methylcarbamoyl-thymidines, and their 2'-methoxy, 2'-amino or 2'-acetamido analogs were prepared. Their duplex-forming ability with DNA and RNA complements was evaluated by UV melting experiments. Interestingly, 4'-carboxythymidine existing in the S-type sugar conformation was found to lead to an increase in the stability of the duplex formed with RNA complements compared to natural thymidine.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
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