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Abstract
Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Geeta Meher
- Spring Bank Pharmaceuticals, Inc, Milford, Massachusetts
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2
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Hari Y, Ijitsu S, Akabane-Nakata M, Yoshida T, Obika S. Kinetic study of the binding of triplex-forming oligonucleotides containing partial cationic modifications to double-stranded DNA. Bioorg Med Chem Lett 2014; 24:3046-9. [PMID: 24865415 DOI: 10.1016/j.bmcl.2014.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 05/08/2014] [Accepted: 05/10/2014] [Indexed: 01/21/2023]
Abstract
Several triplex-forming oligonucleotides (TFOs) partially modified with 2'-O-(2-aminoethyl)- or 2'-O-(2-guanidinoethyl)-nucleotides were synthesized and their association rate constants (kon) with double-stranded DNA were estimated by UV spectrophotometry. Introduction of cationic modifications in the 5'-region of the TFOs significantly increased the kon values compared to that of natural TFO, while no enhancement in the rate of triplex DNA formation was observed when the modifications were in the middle and at the 3'-region. The kon value of a TFO with three adjacent cationic modifications at the 5'-region was found to be 3.4 times larger than that of a natural one. These results provide useful information for overcoming the inherent sluggishness of triplex DNA formation.
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Affiliation(s)
- Yoshiyuki Hari
- Graduate School of Phamaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan.
| | - Shin Ijitsu
- Graduate School of Phamaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
| | - Masaaki Akabane-Nakata
- Graduate School of Phamaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
| | - Takuya Yoshida
- Graduate School of Phamaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Phamaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan.
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3
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Kotikam V, Kumar VA. Synthesis and properties of 2′-O-[R- and S-(2-amino-3-methoxy)propyl] (R-AMP and S-AMP) nucleic acids. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.05.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Prakash TP. An Overview of Sugar-Modified Oligonucleotides for Antisense Therapeutics. Chem Biodivers 2011; 8:1616-41. [DOI: 10.1002/cbdv.201100081] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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5
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Introduction of guanidinium-modified deoxyuridine into the substrate binding regions of DNAzyme 10–23 to enhance target affinity: Implications for DNAzyme design. Bioorg Med Chem Lett 2010; 20:5119-22. [DOI: 10.1016/j.bmcl.2010.07.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/04/2010] [Accepted: 07/07/2010] [Indexed: 12/22/2022]
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6
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Gerrard SR, Edrees MM, Bouamaied I, Fox KR, Brown T. CG base pair recognition within DNA triple helices by modified N-methylpyrrolo-dC nucleosides. Org Biomol Chem 2010; 8:5087-96. [DOI: 10.1039/c0ob00119h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Winkler J, Gilbert M, Kocourková A, Stessl M, Noe CR. 2'-O-Lysylaminohexyl oligonucleotides: modifications for antisense and siRNA. ChemMedChem 2008; 3:102-10. [PMID: 17979170 DOI: 10.1002/cmdc.200700169] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A novel type of oligonucleotide has been developed, characterized by the attachment of a lysyl moiety to a 2'-O-aminohexyl linker. A protected lysine building block was tethered to 2'-O-aminohexyluridine, and the product was converted into the corresponding phosphoramidite. Up to six modified nucleosides were incorporated in dodecamer DNA and RNA oligonucleotides using standard phosphoramidite chemistry. Each of the building blocks contributes one positive charge to the oligonucleotide instead of the negative charge of a wild-type nucleotide. Thermal denaturation profiles indicated a stabilizing effect of 2'-O-lysylaminohexyl chains that was more pronounced in RNA duplexes. Incubation of the oligonucleotides with 5'-exonuclease revealed an exceptionally high stability against enzymatic degradation. Incorporation of up to three modifications into functional antisense and siRNA oligonucleotides targeted at ICAM-1 showed that the gene-silencing activity was higher with an increasing number of lysylaminohexyl nucleotides. Compared with wild-type antisense or siRNA, compounds with three modifications led to equal or higher ICAM-1 downregulation.
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Affiliation(s)
- Johannes Winkler
- Department of Medicinal Chemistry, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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8
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Smicius R, Engels JW. Preparation of Zwitterionic Ribonucleoside Phosphoramidites for Solid-Phase siRNA Synthesis. J Org Chem 2008; 73:4994-5002. [DOI: 10.1021/jo800451m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Romualdas Smicius
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Joachim W. Engels
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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9
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Zatsepin TS, Romanova EA, Oretskaya TS. Synthesis of 2'-O-alkylnucleosides. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc2002v071n06abeh000714] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Højfeldt JW, Blakskjaer P, Gothelf KV. A cleavable amino-thiol linker for reversible linking of amines to DNA. J Org Chem 2007; 71:9556-9. [PMID: 17137397 DOI: 10.1021/jo0619736] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A cleavable heterobifunctional cross-linker for the reversible conjugation of amines to thiol-modified DNA has been developed and tested. The succinimidyl 2-(vinylsulfonyl)ethyl carbonate (SVEC) was prepared in three steps and tested for its ability to react with amines and thiols. The linker was efficient for binding leucine to a thiol-modified DNA sequence and for releasing the amino acid at pH 11.8.
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Affiliation(s)
- Jonas W Højfeldt
- Center for Catalysis and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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11
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Prakash TP, Püschl A, Manoharan M. N,N'-Bis-(2-(cyano)ethoxycarbonyl)-2-methyl-2-thiopseudourea: a guanylating reagent for synthesis of 2'-O-[2-(Guanidinium)ethyl]-modified oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:149-59. [PMID: 17365794 DOI: 10.1080/15257770601112705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A guanylating reagent, N,N'-bis-(2-(cyano)ethoxycarbonyl)-2-thiopseudourea, was synthesized and used for synthesis of 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modified oligonucleotides. A convenient deprotection method for the 2'-O-GE oligonucleotides was developed.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., Carlsbad, California 92008. USA
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12
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Danion A, Brochu H, Martin Y, Vermette P. Fabrication and characterization of contact lenses bearing surface-immobilized layers of intact liposomes. J Biomed Mater Res A 2007; 82:41-51. [PMID: 17265438 DOI: 10.1002/jbm.a.31147] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Intact liposomes were immobilized onto soft contact lenses. In the first step, polyethylenimine was covalently bounded onto the hydroxyl groups available on the surface of a commercial contact lens (Hioxifilcon B). Then, NHS-PEG-biotin molecules were bounded onto the surface amine groups by carbodiimide chemistry. NeutrAvidin were bounded onto the PEG-biotin layer. Liposomes containing PEG-biotinylated lipids were docked onto the surface-immobilized NeutrAvidin. Consecutive addition of further NeutrAvidin and liposome layers enabled fabrication of multilayers. Multilayers of liposomes were also produced by exposing contact lenses coated with NeutrAvidin to liposome aggregates produced by the addition of free biotin in solution. XPS revealed the immobilization of the different layers. By blocking with excess biotin surface-immobilized NeutrAvidin on contact lenses bearing PEG-biotin layers produced under cloud point conditions, ELISA showed that the docking of NeutrAvidin was dependent on biotin-NeutrAvidin affinity binding, with little evidence for nonspecific physisorption; however, it was not possible to differentiate specific versus nonspecific binding of NeutrAvidin attached onto PEG-biotin layers grafted without cloud point conditions. AFM imaging revealed liposome sizes of 106 and 155 nm for layers of liposomes produced (i) by the consecutive addition of further NeutrAvidin and liposomes and (ii) by the exposure of NeutrAvidin-coated contact lenses to liposome aggregates, respectively. The release kinetics of a fluorescent dye demonstrated that intact liposomes had been immobilized onto contact lens surfaces. The stability of surface-immobilized liposomes onto contact lens surfaces showed temperature dependence. Surface-bound liposomes can be stored up to 1 month at 4 degrees C with little release of their content.
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Affiliation(s)
- Anne Danion
- Laboratoire de Bioingénierie et de Biophysique de l'Université de Sherbrooke, Department of Chemical Engineering, Université de Sherbrooke, 2500, Blvd de l'Université, Sherbrooke, Québec, Canada J1K 2R1
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13
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Deglane G, Abes S, Michel T, Prévot P, Vives E, Debart F, Barvik I, Lebleu B, Vasseur JJ. Impact of the guanidinium group on hybridization and cellular uptake of cationic oligonucleotides. Chembiochem 2006; 7:684-92. [PMID: 16518865 DOI: 10.1002/cbic.200500433] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The grafting of cationic groups to synthetic oligonucleotides (ONs) in order to reduce the charge repulsion between the negatively charged strands of a duplex or triplex, and consequently to increase a complex's stability, has been extensively studied. Guanidinium groups, which are highly basic and positively charged over a wide pH range, could be an efficient ON modification to enhance their affinity for nucleic acid targets and to improve cellular uptake. A straightforward post-synthesis method to convert amino functions attached to ONs (on sugar, nucleobase or backbone) into guanidinium tethers has been perfected. In comparison to amino groups, such cationic groups anchored to alpha-oligonucleotide phosphoramidate backbones play important roles in duplex stability, particularly with RNA targets. This high affinity could be explained by dual recognition resulting from Watson-Crick or Hoogsteen base pairing combined with cationic/anionic backbone recognition between strands involving H-bond formation and salt bridging. Molecular-dynamics simulations corroborate interactions between the cationic backbones of the alpha-ONs and the anionic backbones of the nucleic acid targets. Moreover, ONs with guanidinium modification increased cellular uptake relative to negatively charged ONs. The cellular localization of these new cationic phosphoramidate ONs is mainly cytoplasmic. The uptake of these ON analogues might occur through endocytosis.
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Affiliation(s)
- Gaëlle Deglane
- LCOBS, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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14
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Noe CR, Winkler J, Urban E, Gilbert M, Haberhauer G, Brunar H. Zwitterionic oligonucleotides: a study on binding properties of 2'-O-aminohexyl modifications. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1167-85. [PMID: 16270660 DOI: 10.1081/ncn-200067400] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
2'-O-Aminohexyl side chains provide excellent conditions for zwitterionic interstrand and intrastrand interactions of oligonucleotides. 2'-O-Aminoalkylated phosphoramidites of adenosine and uridine were synthesized and incorporated in increasing number into homo adenosine and homo uridine/thymidine dodecamers, respectively. CD spectra of these dodecamers with complementary sense DNA exhibited a B-DNA type structure. While duplex stability values of all tested oligonucleotides were lower than those of the native oligonucleotides, they were significantly higher than those of 2'-O-heptyl modified oligonucleotides. The destabilization amounted to 0.9, 1.5, and 2.7 degrees C per modification for 2'-O-aminohexyl adenosine, 2'-O-aminohexyl uridine, and 2'-O-heptyl adenosine substitutions. These findings are pointing to a duplex stabilizing effect of the interaction of side chain amino groups with backbone phosphoric acid.
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Affiliation(s)
- Christian R Noe
- Department für Medizinische/Pharmazeutische Chemie, Universität Wien, Pharmaziezentrum, Althanstrasse 14, Wien 1090, Austria.
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15
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Abstract
A new method for synthesizing oligonucleotide peptide conjugates by an in-line approach is presented. A phosphorothioate oligonucleotide with the sequence of bcl-2 targeted Oblimersen by employing a modified 2'-amino-2'-desoxy-uridine nucleotide bearing a succinyl linker at the 2' position was prepared. The carboxyl group was protected for solid-phase synthesis as the benzyl ester. Ester cleavage was afforded by a phase transfer reaction using palladium nanoparticles as catalyst and cyclohexadiene as hydrogen donor. Short tails of up to three lysyl residues were conjugated to the oligonucleotide by an inverse stepwise peptide synthesis. The conjugates were characterized by HPLC, mass spectrometry, and circular dichroism. Influence of lysyl tails on CD spectra were minimal. Melting profiles revealed only minimal destabilizing effects on duplexes by conjugation of peptides.
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Affiliation(s)
- Johannes Winkler
- Department of Medicinal Chemistry, Universität Wien, Althanstrasse 14, 1090 Wien, Austria
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16
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Jin S, Miduturu CV, McKinney DC, Silverman SK. Synthesis of amine- and thiol-modified nucleoside phosphoramidites for site-specific introduction of biophysical probes into RNA. J Org Chem 2005; 70:4284-99. [PMID: 15903302 DOI: 10.1021/jo050061l] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For studies of RNA structure, folding, and catalysis, site-specific modifications are typically introduced by solid-phase synthesis of RNA oligonucleotides using nucleoside phosphoramidites. Here, we report the preparation of two complete series of RNA nucleoside phosphoramidites; each has an appropriately protected amine or thiol functional group. The first series includes each of the four common RNA nucleotides, U, C, A, and G, with a 2'-(2-aminoethoxy)-2'-deoxy substitution (i.e., a primary amino group tethered to the 2'-oxygen by a two-carbon linker). The second series encompasses the four common RNA nucleotides, each with the analogous 2'-(2-mercaptoethoxy)-2'-deoxy substitution (i.e., a tethered 2'-thiol). The amines are useful for acylation and reductive amination reactions, and the thiols participate in displacement and oxidative cross-linking reactions, among other likely applications. The new phosphoramidites will be particularly valuable for enabling site-specific introduction of biophysical probes and constraints into RNA.
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Affiliation(s)
- Shengxi Jin
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA
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17
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Prakash TP, Püschl A, Lesnik E, Mohan V, Tereshko V, Egli M, Manoharan M. 2'-O-[2-(guanidinium)ethyl]-modified oligonucleotides: stabilizing effect on duplex and triplex structures. Org Lett 2005; 6:1971-4. [PMID: 15176796 DOI: 10.1021/ol049470e] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] Oligonucleotides with a novel 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modification have been synthesized using a novel protecting group strategy for the guanidinium group. This modification enhances the binding affinity of oligonucleotides to RNA as well as duplex DNA (DeltaT(m) 3.2 degrees C per modification). The 2'-O-GE modified oligonucleotides exhibited exceptional resistance to nuclease degradation. The crystal structure of a palindromic duplex formed by a DNA oligonucleotide with a single 2'-O-GE modification was solved at 1.16 A resolution.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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18
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Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)01104-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Prhavc M, Prakash TP, Minasov G, Cook PD, Egli M, Manoharan M. 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects. Org Lett 2003; 5:2017-20. [PMID: 12790517 DOI: 10.1021/ol0340991] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[structure: see text] Oligonucleotides with a novel, 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] (2'-O-DMAEOE) modification have been synthesized. This modification, a cationic analogue of the 2'-O-(2-methoxyethyl) (2'-O-MOE) modification, exhibits high binding affinity to target RNA (but not to DNA) and exceptional resistance to nuclease degradation. Analysis of the crystal structure of a self-complementary oligonucleotide containing a single 2'-O-DMAEOE modification explains the importance of charge factors and gauche effects on the observed antisense properties. 2'-O-DMAEOE modified oligonucleotides are ideal candidates for antisense drugs.
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Affiliation(s)
- Marija Prhavc
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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20
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Zhu L, dos Santos O, Seeman NC, Canary JW. Reaction of N3-benzoyl-3',5'-O-(di-tert-butylsilanediyl)uridine with hindered electrophiles: intermolecular N3 to 2'-O protecting group transfer. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002; 21:723-35. [PMID: 12502286 DOI: 10.1081/ncn-120015728] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The compound N3-benzoyl-3',5'-O-(di-tert-butylsilanediyl)uridine 2 was alkylated with various alkyl iodides in CH3CN in the presence of base. Normal 2'-O-alkylated products were obtained with methyl or benzyl iodide. If hindered alkyl iodides with beta-branching such as 2-ethylbutyl iodide were used as electrophiles under the same conditions, N3-alkyl-2'-O-benzoyl uridine derivatives were produced. This unexpected transformation is usually dormant with reactive alkylating agents, but expressed with sterically hindered, less reactive electrophiles. This unwanted reaction gives isomeric products whose spectra differ in only subtle ways from target compounds.
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Affiliation(s)
- Lei Zhu
- Department of Chemistry, New York University, New York, NY 10003, USA
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21
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Postsynthetic guanidinylation of primary amino groups in the minor and major grooves of oligonucleotides. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01732-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Prakash TP, Kawasaki AM, Fraser AS, Vasquez G, Manoharan M. Synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] modified nucleosides and oligonucleotides. J Org Chem 2002; 67:357-69. [PMID: 11798305 DOI: 10.1021/jo0103975] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.
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Affiliation(s)
- Thazha P Prakash
- Department of Medicinal Chemistry, Isis Pharmaceuticals Inc., 2292 Faraday Avenue, Carlsbad, California 92008, USA
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23
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24
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Chen T, Fu J, Greenberg MM. Synthesis and deprotection of oligonucleotides under aprotic conditions. Org Lett 2000; 2:3691-4. [PMID: 11073677 DOI: 10.1021/ol006604p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotides containing an alkali-labile nucleotide are synthesized and deprotected using a synthetic method that eliminates the use of Bronsted acid and base. The development of a new family of exocyclic amine-protecting groups is an integral component of this approach.
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Affiliation(s)
- T Chen
- Department of Chemistry, Colorado State University, Ft. Collins, Colorado 80523, USA
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25
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Prakash TP, Manoharan M, Fraser AS, Kawasaki AM, Lesnik EA, Owens SR. Zwitterionic oligonucleotides with 2′-O-[3-(N,N-dimethylamino)propyl]-RNA modification: synthesis and properties. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)00703-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Hwang JT, Greenberg MM. Synthesis of modified oligodeoxyribonucleotides on a solid-phase support via derivatization of a selectively revealed 2'-amino-2'-deoxyuridine. Org Lett 1999; 1:2021-4. [PMID: 10836059 DOI: 10.1021/ol991196e] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[formula: see text] High yields of oligodeoxyribonucleotides modified at the C2'-position of site specifically incorporated 2'-amino-2'-deoxyuridine are obtained by photolytically unmasking the nucleophile in an otherwise protected solid-phase support-bound biopolymer.
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Affiliation(s)
- J T Hwang
- Department of Chemistry, Colorado State University, Fort Collins 80523, USA
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27
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Manoharan M. 2'-carbohydrate modifications in antisense oligonucleotide therapy: importance of conformation, configuration and conjugation. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:117-30. [PMID: 10807002 DOI: 10.1016/s0167-4781(99)00138-4] [Citation(s) in RCA: 246] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The 2'-position of the carbohydrate moiety has proven to be a fertile position for oligonucleotide modifications for antisense technology. The 2'-modifications exhibit high binding affinity to target RNA, enhanced chemical stability and nuclease resistance and increased lipophilicity. All high binding affinity 2'-modifications have C3'-endo sugar pucker. In addition to gauche effects, charge effects are also important in determining the level of their nuclease resistance. Pharmacokinetic properties of oligonucleotides are altered by 2'-conjugates. For certain modifications (e.g., 2'-F), the configuration at the 2'-position, arabino vs. ribo, determines their ability to activate the enzyme RNase H.
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Affiliation(s)
- M Manoharan
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Carlsbad, CA 92008, USA.
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