1
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Duchamp E, Vasquez G, Firoozi N, Freestone GC, Oestergaard M, Seth PP, Hanessian S. Towards combining backbone and sugar constraint in 3'-3' bis-phosphonate tethered 2'-4' bridged LNA oligonucleotide trimers. RSC Adv 2024; 14:23583-23591. [PMID: 39070250 PMCID: PMC11276400 DOI: 10.1039/d4ra04277h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024] Open
Abstract
Therapeutic oligonucleotides are chemically modified to enhance their drug-like properties - including binding affinity for target RNA. Many nucleic acid analogs that enhance RNA binding affinity constrain the furanose sugar in an RNA-like sugar pucker. The improvements in binding affinity result primarily from increased off-rates with minimal effects on on-rates for hybridization. To identify alternate chemical modification strategies that can modulate on- and off-rates for oligonucleotide hybridization, we hypothesized that extending conformational restraint across multiple nucleotides could modulate hybridization kinetics by restricting rotational freedom of the sugar-phosphate backbone. As part of that effort, we recently reported that using hydrocarbon tethers to bridge adjacent phosphodiester linkages as phosphonate tethered bridges can pre-organize nucleic acids in conformations conducive for Watson-Crick base-pairing and modulate hybridization kinetics. In this report, we describe the synthesis of locked nucleic acid (LNA) trimers linked through alkylphosphonate tethers which restrict conformation of the furanose sugar in addition to restricting conformational mobility of the sugar-phosphate backbone across three nucleotide units.
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Affiliation(s)
- Edouard Duchamp
- Department of Chemistry, Université de Montréal Québec H3C 3J7 Canada
| | - Guillermo Vasquez
- Department of Medicinal Chemistry, Ionis Pharmaceuticals Carlsbad CA 92010 USA
| | - Neda Firoozi
- Department of Chemistry, Université de Montréal Québec H3C 3J7 Canada
| | - Graeme C Freestone
- Department of Medicinal Chemistry, Ionis Pharmaceuticals Carlsbad CA 92010 USA
| | - Michael Oestergaard
- Department of Medicinal Chemistry, Ionis Pharmaceuticals Carlsbad CA 92010 USA
| | - Punit P Seth
- Alnylam Pharmaceuticals 675 West Kendall St Cambridge MA 0214 USA
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal Québec H3C 3J7 Canada
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
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2
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Traoré D, Biecher E, Mallet M, Rouanet S, Vasseur JJ, Smietana M, Dupouy C. Synthesis and properties of RNA constrained by a 2'-O-disulfide bridge. ChemistryOpen 2024:e202300232. [PMID: 38200655 DOI: 10.1002/open.202300232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Indexed: 01/12/2024] Open
Abstract
We recently reported the properties of RNA hairpins constrained by a dimethylene (DME) disulfide (S-S) linker incorporated between two adjacent nucleosides in the loop and showed that this linker locked the hairpin conformation thus disturbing the duplex/hairpin equilibrium. We have now investigated the influence of the length of the linker and synthesized oligoribonucleotides containing diethylene (DEE) and dipropylene (DPE) S-S bridges. This was achieved via the preparation of building blocks, namely 2'-O-acetylthioethyl (2'-O-AcSE) and 2'-O-acetylthiopropyl (2'-O-AcSP) uridine phosphoramidites, which were successfully incorporated into RNA sequences. Thermal denaturation analysis revealed that the DEE and DPE disulfide bridges destabilize RNA duplexes but do not disrupt the hairpin conformation. Furthermore, our investigation of the duplex/hairpin equilibrium indicated that sequences modified with DME and DEE S-S linkers predominantly lock the hairpin form, whereas the DPE S-S linker provides flexibility. These findings highlight the potential of S-S linkers to study RNA interactions.
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Affiliation(s)
- Diallo Traoré
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Elisa Biecher
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Manon Mallet
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Sonia Rouanet
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | | | - Michael Smietana
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Christelle Dupouy
- CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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3
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Osawa T, Akino T, Obika S. Synthesis, Duplex-Forming Ability, and Enzymatic Stability of Oligonucleotides Modified with Amide-Linked Dinucleotides Containing a 3',4'-Tetrahydropyran-Bridged Nucleic Acid. J Org Chem 2024; 89:269-280. [PMID: 38064209 DOI: 10.1021/acs.joc.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Replacement of a phosphodiester linkage with an amide linkage can improve the binding affinity of oligonucleotides to complementary RNA and their stability toward nucleases. In addition, restricting the conformation of the sugar moiety and the phosphate backbone in oligonucleotides effectively improves duplex stability. In this study, we designed amide-linked dinucleotides containing a 3',4'-tetrahydropyran-bridged nucleic acid (3',4'-tpBNA) with a constrained sugar conformation as well as a torsion angle ε. Phosphoramidites of the designed dinucleotides were synthesized and incorporated into oligonucleotides. Conformational analysis of the synthesized dinucleotides showed that the sugar conformation of the S-isomer of the amide-linked dinucleotide containing 3',4'-tpBNA was N-type, which has the same conformation as that of the RNA duplex, while that of another R-isomer was S-type. Tm analysis indicated that the oligonucleotides containing the synthesized S-isomer showed RNA-selective hybridizing ability, although their duplex-forming ability was slightly inferior to that of natural oligonucleotides. Interestingly, the stability of the oligonucleotides toward endonucleases was significantly improved by modification with the two types of amide-linked dinucleotides developed in this study.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Taiki Akino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
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4
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Yamaguchi T, Horie N, Aoyama H, Kumagai S, Obika S. Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Nucleic Acids Res 2023; 51:7749-7761. [PMID: 37462081 PMCID: PMC10450189 DOI: 10.1093/nar/gkad608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/28/2023] [Accepted: 07/09/2023] [Indexed: 08/26/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are becoming a promising class of drugs for treating various diseases. Over the past few decades, many modified nucleic acids have been developed for application to ASOs, aiming to enhance their duplex-forming ability toward cognate mRNA and improve their stability against enzymatic degradations. Modulating the sugar conformation of nucleic acids by substituting an electron-withdrawing group at the 2'-position or incorporating a 2',4'-bridging structure is a common approach for enhancing duplex-forming ability. Here, we report on incorporating an N-tert-butylguanidinium group at the 2',4'-bridging structure, which greatly enhances duplex-forming ability because of its interactions with the minor groove. Our results indicated that hydrophobic substituents fitting the grooves of duplexes also have great potential to increase duplex-forming ability.
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Affiliation(s)
- Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naohiro Horie
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Aoyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shinji Kumagai
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Shonan Health Innovation Park, 2-26-1 Muraoka-Higashi, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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5
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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6
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Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:molecules26195925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
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7
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Vasquez G, Freestone GC, Wan WB, Low A, De Hoyos CL, Yu J, Prakash TP, Ǿstergaard ME, Liang XH, Crooke ST, Swayze EE, Migawa MT, Seth PP. Site-specific incorporation of 5'-methyl DNA enhances the therapeutic profile of gapmer ASOs. Nucleic Acids Res 2021; 49:1828-1839. [PMID: 33544849 PMCID: PMC7913697 DOI: 10.1093/nar/gkab047] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 01/01/2023] Open
Abstract
We recently showed that site-specific incorporation of 2′-modifications or neutral linkages in the oligo-deoxynucleotide gap region of toxic phosphorothioate (PS) gapmer ASOs can enhance therapeutic index and safety. In this manuscript, we determined if introducing substitution at the 5′-position of deoxynucleotide monomers in the gap can also enhance therapeutic index. Introducing R- or S-configured 5′-Me DNA at positions 3 and 4 in the oligodeoxynucleotide gap enhanced the therapeutic profile of the modified ASOs suggesting a different positional preference as compared to the 2′-OMe gap modification strategy. The generality of these observations was demonstrated by evaluating R-5′-Me and R-5′-Ethyl DNA modifications in multiple ASOs targeting HDAC2, FXI and Dynamin2 mRNA in the liver. The current work adds to a growing body of evidence that small structural changes can modulate the therapeutic properties of PS ASOs and ushers a new era of chemical optimization with a focus on enhancing the therapeutic profile as opposed to nuclease stability, RNA-affinity and pharmacokinetic properties. The 5′-methyl DNA modified ASOs exhibited excellent safety and antisense activity in mice highlighting the therapeutic potential of this class of nucleic acid analogs for next generation ASO designs.
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Affiliation(s)
- Guillermo Vasquez
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - W Brad Wan
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Audrey Low
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Jinghua Yu
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | | | - Xue-Hai Liang
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Eric E Swayze
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Michael T Migawa
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Punit P Seth
- Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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8
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Salinas JC, Seth PP, Hanessian S. Design And Synthesis Of An Azabicyclic Nucleoside Phosphoramidite For Oligonucleotide Antisense Constructs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:384-406. [PMID: 31380707 DOI: 10.1080/15257770.2019.1646916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We report the synthesis and biophysical evaluation of an azabicycle dinucleotide with restricted γ, β, and ε torsion angles, featuring the introduction of a piperidine ring that locks the conformation of the nucleoside into an RNA-type nucleic acid. The conceptual basis of the design is predicated upon the notion that the conformation of the phosphate group linking two RNA nucleotides can be approximated with an azabicyclic phosphoramidite which may also benefit from a unique stereoelectronic effect.
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Affiliation(s)
- Juan C Salinas
- Department of Chemistry, Université de Montréal, Downtown Station, Montréal, P.O. Box 6128, Canada QC H3C 3J7
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Downtown Station, Montréal, P.O. Box 6128, Canada QC H3C 3J7
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9
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Escudier JM, Payrastre C, Gerland B, Tarrat N. Convertible and conformationally constrained nucleic acids (C 2NAs). Org Biomol Chem 2019; 17:6386-6397. [PMID: 31210235 DOI: 10.1039/c9ob01150a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.
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Affiliation(s)
- Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, Toulouse 31055, France
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10
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Salinas JC, Yu J, Østergaard M, Seth PP, Hanessian S. Conception and Synthesis of Oxabicyclic Nucleoside Phosphonates as Internucleotidic Phosphate Surrogates in Antisense Oligonucleotide Constructs. Org Lett 2018; 20:5296-5299. [PMID: 30146887 DOI: 10.1021/acs.orglett.8b02233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The stereocontrolled synthesis of a novel oxabicyclic nucleoside phosphonate comprising a perhydrofuropyran core unit was achieved. It was incorporated in an oligonucleotide sequence as a 5'-3' phosphonate-phosphate insert, and the stability properties of the resulting duplex were measured. The oxabicyclic nucleoside framework was designed so as to restrict rotation around angles γ, δ, and ε of a natural nucleoside.
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Affiliation(s)
- Juan C Salinas
- Department of Chemistry , Université de Montréal , P.O. Box 6128, Downtown Station , Montréal , QC H3C 3J7 , Canada
| | - Jeff Yu
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , 2855 Gazelle Court , Carlsbad , California 92010 , United States
| | - Michael Østergaard
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , 2855 Gazelle Court , Carlsbad , California 92010 , United States
| | - Punit P Seth
- Department of Medicinal Chemistry , Ionis Pharmaceuticals , 2855 Gazelle Court , Carlsbad , California 92010 , United States
| | - Stephen Hanessian
- Department of Chemistry , Université de Montréal , P.O. Box 6128, Downtown Station , Montréal , QC H3C 3J7 , Canada
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11
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Giacometti RD, Salinas JC, Østergaard ME, Swayze EE, Seth PP, Hanessian S. Design, synthesis, and duplex-stabilizing properties of conformationally constrained tricyclic analogues of LNA. Org Biomol Chem 2016; 14:2034-40. [PMID: 26765794 DOI: 10.1039/c5ob02576a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The design, synthesis and biophysical evaluation of two highly-constrained tricyclic analogues of locked nucleic acid (LNA), which restrict rotation around the C4'-C5'-exocyclic bond (torsion angle γ) and enhance hydrophobicity in the minor groove and along the major groove, are reported. A structural model that provides insights into the sugar-phosphate backbone conformations required for efficient hybridization to complementary nucleic acids is also presented.
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Affiliation(s)
- Robert D Giacometti
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada.
| | - Juan C Salinas
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada.
| | - Michael E Østergaard
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA.
| | - Eric E Swayze
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA.
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA.
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Downtown Station, Montréal, QC H3C 3J7, Canada.
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12
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Abstract
Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.
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Affiliation(s)
- W Brad Wan
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Punit P Seth
- Department of Medicinal Chemistry, Ionis Pharmaceuticals , 2855 Gazelle Court, Carlsbad, California 92010, United States
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13
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Østergaard ME, Gerland B, Escudier JM, Swayze EE, Seth PP. Differential effects on allele selective silencing of mutant huntingtin by two stereoisomers of α,β-constrained nucleic acid. ACS Chem Biol 2014; 9:1975-9. [PMID: 25050989 DOI: 10.1021/cb5003027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We describe the effects of introducing two epimers of neutral backbone α,β-constrained nucleic acid (CNA) on the activity and allele selectivity profile of RNase H active antisense oligonucleotides (ASOs) targeting a single nucleotide polymorphism (SNP) for the treatment of Huntington's disease (HD). ASOs modified with both isomers of α,β-CNA in the gap region showed good activity versus the mutant allele, but one isomer showed improved selectivity versus the wild-type allele. Analysis of the human RNase H cleavage patterns of α,β-CNA modified ASOs versus matched and mismatched RNA revealed that both isomers support RNase H cleavage on the RNA strand across from the site of incorporation in the ASO--an unusual observation for a neutral linkage oligonucleotide modification. Interestingly, ASOs modified with (R)- and (S)-5'-hydroxyethyl DNA (RHE and SHE respectively) formed by partial hydrolysis of the dioxaphosphorinane ring system in α,β-CNA also showed good activity versus the mutant allele but an improved selectivity profile was observed for the RHE modified ASO. Our observations further support the profiling of neutral and 5'-modified nucleic acid analogs as tools for gene silencing applications.
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Affiliation(s)
- Michael E. Østergaard
- Isis Pharmaceuticals
Inc. 2855 Gazelle Court, Carlsbad, California 92011, United States
| | - Béatrice Gerland
- Laboratoire
de Synthèse et Physico-Chimie de Molécules d’Intérêt
Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route
de Narbonne, Toulouse F-31062, France
| | - Jean-Marc Escudier
- Laboratoire
de Synthèse et Physico-Chimie de Molécules d’Intérêt
Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 Route
de Narbonne, Toulouse F-31062, France
| | - Eric E. Swayze
- Isis Pharmaceuticals
Inc. 2855 Gazelle Court, Carlsbad, California 92011, United States
| | - Punit P. Seth
- Isis Pharmaceuticals
Inc. 2855 Gazelle Court, Carlsbad, California 92011, United States
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14
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Pathigoolla A, Sureshan KM. Synthesis of Triazole-linked Homonucleoside Polymers through Topochemical Azide-Alkyne Cycloaddition. Angew Chem Int Ed Engl 2014; 53:9522-5. [DOI: 10.1002/anie.201404797] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 12/24/2022]
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15
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Pathigoolla A, Sureshan KM. Synthesis of Triazole-linked Homonucleoside Polymers through Topochemical Azide-Alkyne Cycloaddition. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404797] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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16
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Seth PP, Swayze EE. Unnatural Nucleoside Analogs for Antisense Therapy. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527676545.ch12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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17
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Lefoix M, Mathis G, Kleinmann T, Truffert JC, Asseline U. Pyrazolo[1,5-a]-1,3,5-triazine C-nucleoside as deoxyadenosine analogue: synthesis, pairing, and resistance to hydrolysis. J Org Chem 2014; 79:3221-7. [PMID: 24649913 DOI: 10.1021/jo5000253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthesis of a pyrazolo[1,5-a]-1,3,5-triazine C-nucleoside (dA(PT)), designed to form two hydrogen bonds with a complementary dT residue, is reported. Oligonucleotides including this dA nucleoside analogue possess base-pairing properties similar to those of the parent oligonucleotide. This dA nucleoside analogue is more resistant to acid-catalyzed hydrolysis than dA.
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Affiliation(s)
- Myriam Lefoix
- NucleoSyn. Pépinières d'entreprises - Centre Innovation 16, Rue Léonard de Vinci 45074 Orléans Cedex 2, France
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Gerland B, Millard P, Dupouy C, Renard BL, Escudier JM. Stabilization of hairpins and bulged secondary structures of nucleic acids by single incorporation of α,β-D-CNA featuring a gauche(+) alpha torsional angle. RSC Adv 2014. [DOI: 10.1039/c4ra09639h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A constrained dinucleotide unit featuring a gauche(+) alpha torsional angle configuration was used to stabilize DNA hairpin or bulged structures.
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Affiliation(s)
- Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Pierre Millard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Christelle Dupouy
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Brice-Loïc Renard
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique
- UMR 5068 CNRS
- Université Paul Sabatier
- 31062 Toulouse Cedex 9, France
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19
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Hanessian S, Wagger J, Merner BL, Giacometti RD, Ostergaard ME, Swayze EE, Seth PP. A constrained tricyclic nucleic acid analogue of α-L-LNA: investigating the effects of dual conformational restriction on duplex thermal stability. J Org Chem 2013; 78:9064-75. [PMID: 23937256 DOI: 10.1021/jo401170y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A constrained tricyclic analogue of α-L-LNA (2), which contains dual modes of conformational restriction about the ribose sugar moiety, has been synthesized and characterized by X-ray crystallography. Thermal denaturation experiments of oligonucleotide sequences containing this tricyclic α-L-LNA analogue (α-L-TriNA 2, 5) indicate that this modification is moderately stabilizing when paired with complementary DNA and RNA, but less stabilizing than both α-L-LNA (2) and α-L-TriNA 1 (4).
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal , Montréal, QC, H3C 3J7, Canada
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20
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Ulrich S, Dumy P, Boturyn D, Renaudet O. Engineering of biomolecules for sensing and imaging applications. J Drug Deliv Sci Technol 2013. [DOI: 10.1016/s1773-2247(13)50001-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Dioxaphosphorinane-constrained nucleic Acid dinucleotides as tools for structural tuning of nucleic acids. J Nucleic Acids 2012; 2012:215876. [PMID: 23150809 PMCID: PMC3488415 DOI: 10.1155/2012/215876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/02/2012] [Indexed: 01/03/2023] Open
Abstract
We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles α to ζ defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of α,β-D-CNA exhibiting wether B-type canonical values or not.
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22
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Hanessian S, Schroeder BR, Giacometti RD, Merner BL, Ostergaard M, Swayze EE, Seth PP. Structure-based design of a highly constrained nucleic acid analogue: improved duplex stabilization by restricting sugar pucker and torsion angle γ. Angew Chem Int Ed Engl 2012; 51:11242-5. [PMID: 22915274 DOI: 10.1002/anie.201203680] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/06/2012] [Indexed: 12/22/2022]
Abstract
Dual conformational restriction: a new, highly constrained modification of the α-L-locked nucleic acid (α-L-LNA) scaffold that locks the sugar furanose ring in an N-type configuration and also restricts rotation around torsion angle γ was synthesized. This new modification increases the thermostability of an oligonucleotide duplex compared to using a single mode of constraint alone.
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23
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Hanessian S, Schroeder BR, Giacometti RD, Merner BL, Østergaard M, Swayze EE, Seth PP. Structure-Based Design of a Highly Constrained Nucleic Acid Analogue: Improved Duplex Stabilization by Restricting Sugar Pucker and Torsion Angleγ. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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24
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Martínez O, Ecochard V, Mahéo S, Gross G, Bodin P, Teissié J, Escudier JM, Paquereau L. α,β-D-constrained nucleic acids are strong terminators of thermostable DNA polymerases in polymerase chain reaction. PLoS One 2011; 6:e25510. [PMID: 21991314 PMCID: PMC3185000 DOI: 10.1371/journal.pone.0025510] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 09/07/2011] [Indexed: 11/18/2022] Open
Abstract
(S(C5'), R(P)) α,β-D- Constrained Nucleic Acids (CNA) are dinucleotide building blocks that can feature either B-type torsional angle values or non-canonical values, depending on their 5'C and P absolute stereochemistry. These CNA are modified neither on the nucleobase nor on the sugar structure and therefore represent a new class of nucleotide with specific chemical and structural characteristics. They promote marked bending in a single stranded DNA so as to preorganize it into a loop-like structure, and they have been shown to induce rigidity within oligonucleotides. Following their synthesis, studies performed on CNA have only focused on the constraints that this family of nucleotides introduced into DNA. On the assumption that bending in a DNA template may produce a terminator structure, we investigated whether CNA could be used as a new strong terminator of polymerization in PCR. We therefore assessed the efficiency of CNA as a terminator in PCR, using triethylene glycol phosphate units as a control. Analyses were performed by denaturing gel electrophoresis and several PCR products were further analysed by sequencing. The results showed that the incorporation of only one CNA was always skipped by the polymerases tested. On the other hand, two CNA units always stopped proofreading polymerases, such as Pfu DNA polymerase, as expected for a strong replication terminator. Non-proofreading enzymes, e.g. Taq DNA polymerase, did not recognize this modification as a strong terminator although it was predominantly stopped by this structure. In conclusion, this first functional use of CNA units shows that these modified nucleotides can be used as novel polymerization terminators of proofreading polymerases. Furthermore, our results lead us to propose that CNA and their derivatives could be useful tools for investigating the behaviour of different classes of polymerases.
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Affiliation(s)
- Olivier Martínez
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté des Sciences et d'Ingénierie, Toulouse, France
| | - Vincent Ecochard
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté des Sciences et d'Ingénierie, Toulouse, France
| | - Sabrina Mahéo
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté des Sciences et d'Ingénierie, Toulouse, France
| | - Grégori Gross
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté des Sciences et d'Ingénierie, Toulouse, France
| | - Pierre Bodin
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté des Sciences et d'Ingénierie, Toulouse, France
| | - Justin Teissié
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté des Sciences et d'Ingénierie, Toulouse, France
| | - Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, Unité Mixte de Recherche 5068, Centre National de la Recherche Scientifique, Toulouse , France
| | - Laurent Paquereau
- Institut de Pharmacologie et de Biologie Structurale, Unité Mixte de Recherche 5089, Centre National de la Recherche Scientifique, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté des Sciences et d'Ingénierie, Toulouse, France
- * E-mail:
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25
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Boissonnet A, Dupouy C, Millard P, Durrieu MP, Tarrat N, Escudier JM. α,β-D-CNA featuring canonical and noncanonical α/β torsional angles behaviours within oligonucleotides. NEW J CHEM 2011. [DOI: 10.1039/c1nj20086k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Seth PP, Allerson CR, Siwkowski A, Vasquez G, Berdeja A, Migawa MT, Gaus H, Prakash TP, Bhat B, Swayze EE. Configuration of the 5'-methyl group modulates the biophysical and biological properties of locked nucleic acid (LNA) oligonucleotides. J Med Chem 2010; 53:8309-18. [PMID: 21058707 DOI: 10.1021/jm101207e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As part of a program aimed at exploring the structure- activity relationships of 2',4'-bridged nucleic acid (BNA) containing antisense oligonucleotides (ASOs), we report the synthesis and biophysical and biological properties of R- and S-5'-Me LNA modified oligonucleotides. We show that introduction of a methyl group in the (S) configuration at the 5'-position is compatible with the high affinity recognition of complementary nucleic acids observed with LNA. In contrast, introduction of a methyl group in the (R) configuration reversed the stabilization effect of LNA. NMR studies indicated that the R-5'-Me group changes the orientation around torsion angle γ from the +sc to the ap range at the nucleoside level, and this may in part be responsible for the poor hybridization behavior exhibited by this modification. In animal experiments, S-5'-Me-LNA modified gapmer antisense olignucleotides showed slightly reduced potency relative to the sequence matched LNA ASOs while improving the therapeutic profile.
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27
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Bell NM, Micklefield J. Chemical modification of oligonucleotides for therapeutic, bioanalytical and other applications. Chembiochem 2010; 10:2691-703. [PMID: 19739190 DOI: 10.1002/cbic.200900341] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Neil M Bell
- School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
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28
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Dupouy C, Millard P, Boissonnet A, Escudier JM. α,β-D-CNA preorganization of unpaired loop moiety stabilizes DNA hairpin. Chem Commun (Camb) 2010; 46:5142-4. [DOI: 10.1039/c0cc00244e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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29
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30
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Dupouy C, Iché-Tarrat N, Durrieu MP, Vigroux A, Escudier JM. Alpha,beta-D-CNA induced rigidity within oligonucleotides. Org Biomol Chem 2008; 6:2849-51. [PMID: 18688476 DOI: 10.1039/b809775e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction of alpha,beta-D-CNA featuring canonical values of the torsional angles alpha and beta within oligonucleotides leads to an overall stabilization and improved rigidity of the duplex DNA as demonstrated by UV experiments, circular dichroism and corroborated by molecular dynamics simulations.
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Affiliation(s)
- Christelle Dupouy
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique UMR 5068 CNRS, Université Paul Sabatier, 31062, Toulouse Cedex 9, France
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31
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Liu Y, Wang R, Ding L, Sha R, Lukeman PS, Canary JW, Seeman NC. Thermodynamic analysis of nylon nucleic acids. Chembiochem 2008; 9:1641-8. [PMID: 18543259 PMCID: PMC2976662 DOI: 10.1002/cbic.200800032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Indexed: 11/08/2022]
Abstract
The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1-5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26 degrees C increase in the thermal transition temperature (T(m)) for five linkages) and RNA (around 15 degrees C increase in T(m) for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised T(m) from less to slightly greater than T(m) of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2'-position of ribose and recovery of stability upon linkage of the side chains.
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Affiliation(s)
- Yu Liu
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Risheng Wang
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Liang Ding
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Ruojie Sha
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Philip S. Lukeman
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - James W. Canary
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
| | - Nadrian C. Seeman
- Department of Chemistry New York University 100 Washington Square E., New York, NY 10003 (USA) Fax: (+1) 212-260-7905
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32
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Synthesis of spiro ɛ,ζ-D-CNA in xylo configuration featuring noncanonical δ/ɛ/ζ torsion angle combination. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.08.098] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Dupouy C, Le Clézio I, Lavedan P, Gornitzka H, Escudier JM, Vigroux A. Diastereoselective Synthesis of Conformationally Restricted Dinucleotides Featuring Canonical and Noncanonical α/β Torsion Angle Combinations(α,β-D-CNA). European J Org Chem 2006. [DOI: 10.1002/ejoc.200600593] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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