1
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Li NS, Koo SC, Piccirilli JA. Synthesis of Oligoribonucleotides Containing a 2'-Amino-5'- S-phosphorothiolate Linkage. J Org Chem 2021; 86:13231-13244. [PMID: 34533968 PMCID: PMC8491167 DOI: 10.1021/acs.joc.1c01059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
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Oligoribonucleotides
containing a photocaged 2′-amino-5′-S-phophorothiolate linkage have potential applications as
therapeutic agents and biological probes to investigate the RNA structure
and function. We envisioned that oligoribonucleotides containing a
2′-amino-5′-S-phosphorothiolate linkage
could provide an approach to identify the general base within catalytic
RNAs by chemogenetic suppression. To enable preliminary tests of this
idea, we developed synthetic approaches to a dinucleotide, trinucleotide,
and oligoribonucleotide containing a photocaged 2′-amino-5′-S-phosphorothiolate linkage. We incorporated the photocaged
2′-amino-5′-S-phosphorothiolate linkage
into an oligoribonucleotide substrate for the hepatitis delta virus
(HDV) ribozyme and investigated the pH dependence of its cleavage
following UV irradiation both in the presence and absence of the ribozyme.
The substrate exhibited a pH-rate profile characteristic of the modified
linkage but reacted slower when bound to the ribozyme. Cleavage inhibition
by the HDV ribozyme could reflect a non-productive ground-state interaction
with the modified substrate’s nucleophilic 2′-NH2 or a poor fit of the modified transition state at the ribozyme’s
active site.
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Affiliation(s)
- Nan-Sheng Li
- Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States
| | - Selene C Koo
- Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States
| | - Joseph A Piccirilli
- Department of Biochemistry & Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States.,Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, Unites States
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2
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Versatile synthesis of 2′-amino-2′-deoxyuridine derivatives with a 2′-amino group carrying linkers possessing a reactive terminal functionality. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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3
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Synthesis and enzymatic incorporation of photolabile dUTP analogues into DNA and their applications for DNA labeling. Bioorg Med Chem 2013; 21:6205-11. [PMID: 23719284 DOI: 10.1016/j.bmc.2013.04.081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 04/26/2013] [Accepted: 04/30/2013] [Indexed: 11/22/2022]
Abstract
Two novel photolabile nucleotide triphosphate (NTP) analogues were synthesized through Sonogashira coupling and their enzymatic incorporation into DNA was evaluated with three different DNA polymerases (Taq, Vent exo- and T4) by polymerase chain reaction. Both nucleotide triphosphate analogues were recognized by these DNA polymerases as substrates for primer extension. Light irradiation of PCR products removed the photolabile group and released the amino and carboxyl moieties. Further site-specific dual-labeling for oligodeoxynucleotides (ODNs) and random labeling for a long DNA construct with fluorophores were successfully achieved with incorporation of the photolabile amine modified deoxyuridine triphosphate (dUnTP).
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4
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Aralov AV, Klykov VN, Chakhmakhcheva OG, Efimov VA. [Monomers containing 2'-o-alkoxymethyl groups as synthons for the synthesis of oligoribonucleotides by the phosphotriester method]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 37:654-61. [PMID: 22332361 DOI: 10.1134/s1068162011050025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A general scheme for the synthesis of ribonucleotide monomers containing alkoxymethyl group in 2'-O-position for the solid-phase phosphotriester oligonucleotide synthesis using O-nucleophilic intramolecular catalysis has been developed. In particular, the monomers containing 2'-O-modifying 2-azidoethoxymethyl, propargyloxymethyl, or 3,4-cyclocarbonatebutoxymethyl groups has been prepared.
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5
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Mori K, Kodama T, Baba T, Obika S. Bridged nucleic acid conjugates at 6'-thiol: synthesis, hybridization properties and nuclease resistances. Org Biomol Chem 2011; 9:5272-9. [PMID: 21643564 DOI: 10.1039/c1ob05469d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The bridged nucleic acid (BNA) containing a thiol at the 6'-position in the bridged structure was synthesized from the disulfide-type BNA and conjugated with various functional molecules via the thioether or the disulfide linkage post-synthetically and efficiently in solution phase. The disulfide-linked conjugate was cleaved under reductive conditions derived from glutathione and an oligonucleotide bearing a free thiol was released smoothly. Conjugated functional molecules had great effects on duplex stability with the DNA complement. In contrast, the molecules little influenced the stability with the RNA complement. Moreover, the oligonucleotides with functional groups at the 6'-position had as high or higher resistances against 3'-exonuclease than phosphorothioate oligonucleotide (S-oligo).
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Affiliation(s)
- Kazuto Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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6
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Lu K, Duan QP, Ma L, Zhao DX. Chemical strategies for the synthesis of peptide-oligonucleotide conjugates. Bioconjug Chem 2010; 21:187-202. [PMID: 19856957 DOI: 10.1021/bc900158s] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The use of synthetic oligonucleotides and their mimics to inhibit gene expression by hybridizing with their target sequences has been hindered by their poor cellular uptake and inability to reach the nucleus. Covalent postsynthesis or solid-phase conjugation of peptides to oligonucleotides offers a possible solution to these problems. As feasible chemistry is a prerequisite for biological studies, development of efficient and reproducible approaches for convenient preparation of peptide-oligonucleotide conjugates has become a subject of considerable importance. The present review gives an account of the main synthetic methods available to prepare covalent conjugation of peptides to oligonucleotides.
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Affiliation(s)
- Kui Lu
- School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China.
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7
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Weisbrod SH, Marx A. Novel strategies for the site-specific covalent labelling of nucleic acids. Chem Commun (Camb) 2008:5675-85. [PMID: 19009049 DOI: 10.1039/b809528k] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.
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Affiliation(s)
- Samuel H Weisbrod
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457, Konstanz, Germany
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8
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Porphyrin conjugated to DNA by a 2'-amido-2'-deoxyuridine linkage. Bioorg Med Chem Lett 2007; 18:850-5. [PMID: 18054487 DOI: 10.1016/j.bmcl.2007.11.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Revised: 11/06/2007] [Accepted: 11/08/2007] [Indexed: 11/21/2022]
Abstract
A porphyrin that contains a single carboxylic acid group was synthesized and coupled to 2'-amino-2'-deoxyuridine. The resultant product contained a free 3' hydroxyl group and a 4,4'-dimethoxytrityl (DMT) protecting group on the 5' hydroxyl of the uridine, making it suitable for use in oligonucleotide synthesis. The 3' H-phosphonate derivative of this molecule was synthesized and used to form a conjugate with a 19 nucleotide sequence of DNA (5'-CCTCCAGTGGAAATCAAGG-3'). This was carried out with the DNA attached at the 3' end to a control pore glass (CPG) substrate, allowing for rapid purification. After removal of the DMT group, an additional three nucleotides were added, leaving the porphyrin as an internal modification. This is the first report of porphyrin attached internally to an oligonucleotide using a hydrogen-bonding nucleoside analog. This allows oligonucleotides to be used as a scaffold for precise positioning of multiple porphyrins within biomimetic arrays.
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9
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Kalek M, Madsen AS, Wengel J. Effective modulation of DNA duplex stability by reversible transition metal complex formation in the minor groove. J Am Chem Soc 2007; 129:9392-400. [PMID: 17616191 DOI: 10.1021/ja071076z] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we describe the reversible changing of DNA duplex thermal stability by exploiting transition metal complexation phenomena. A terpyridine ligand was conjugated to the N2'-atoms of 2'-amino-2'-deoxyuridine and its locked counterpart 2'-amino-LNA, and these metal-complexing monomers were incorporated into oligodeoxyribonucleotides. Upon addition of varying amounts of transition metal ions, the thermal stability of DNA duplexes containing these terpyridine-functionalized units in different constitutions was affected to different degrees (DeltaTm values = -15.5 to +49.0 degrees C, relative to the unmodified duplex). The most pronounced effects were observed when two complexing monomers were positioned in opposite strands. Addition of 1 equiv of Ni2+ to such a system induced extraordinary duplex stabilization. Molecular modeling studies suggest, as an explanation for this phenomenon, formation of nickel-mediated interstrand linkages in the minor groove. Addition of an excess of metal ions resulted in largely decreased Tm values. Alternating addition of metal ions and EDTA demonstrated reversibility of metal ion-induced changes in hybridization strength, proving that the described approach provides an efficient method for duplex stability modulation.
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Affiliation(s)
- Marcin Kalek
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense M, Denmark
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10
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Miller GP, Kool ET. Versatile 5'-functionalization of oligonucleotides on solid support: amines, azides, thiols, and thioethers via phosphorus chemistry. J Org Chem 2004; 69:2404-10. [PMID: 15049637 DOI: 10.1021/jo035765e] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the preparation of conjugates of oligonucleotides is by now commonplace, existing methods (usually utilizing thiols or primary amines) are generally expensive, and often require postsynthetic reaction with the DNA followed by a separate purification. Here we describe simple procedures for a broad set of direct 5'-end (5'-terminal carbon) functionalizations of DNA oligonucleotides while they remain on the synthesizer column. 5'-Iodinated oligonucleotides (prepared by an automated cycle as previously reported) are converted directly to 5'-azides, 5'-thiocarbamates, and alkyl and aryl 5'-thioethers in high yields. Further, we demonstrate high-yielding conversions of DNA-azides to 5'-amines, and of thiocarbamates to 5'-thiols. Finally, we report a new, one-pot conversion of naturally substituted 5'-OH oligonucleotides (again on the solid support) to 5'-amino-oligonucleotides. All of the above reactions are demonstrated in multiple sequence contexts. Most of the procedures are automatable.
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Affiliation(s)
- Gregory P Miller
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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11
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Dioubankova NN, Malakhov AD, Shenkarev ZO, Korshun VA. Oligonucleotides containing new fluorescent 1-phenylethynylpyrene and 9,10-bis(phenylethynyl)anthracene uridine-2′-carbamates: synthesis and properties. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.03.076] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Winkler J, Urban E, Losert D, Wacheck V, Pehamberger H, Noe CR. A novel concept for ligand attachment to oligonucleotides via a 2'-succinyl linker. Nucleic Acids Res 2004; 32:710-8. [PMID: 14757835 PMCID: PMC373351 DOI: 10.1093/nar/gkh229] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conjugation of ligands to antisense oligonucleotides is a promising approach for enhancing their effects. In this report, a new method for synthesizing oligonucleotide conjugates is described. 2'-Amino-2'-deoxy-5'-dimethoxytrityl-uridine was select ively acylated with a succinic acid linker at the 2' position. This compound was incorporated at the 3' end of an oligonucleotide corresponding to the sequence of Oblimersen. The carboxyl group was protected for oligonucleotide synthesis as a benzyl ester, which could be selectively cleaved at the solid phase by a catalytic phase transfer reaction using palladium nanoparticles as catalyst. An oligonucleotide-fluorescein conjugate was prepared by condensation of aminofluorescein. Circular dichroism spectroscopic experiments showed a B-DNA type structure. The melting temperature of the duplex was only slightly lower than that of Oblimersen. Biological activity measured by western blotting resulted in a Bcl-2 target downregulation nearly identical to that of control Oblimersen on human melanoma cells, proving that this method is attractive for the binding of ligands located in the minor groove.
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Affiliation(s)
- Johannes Winkler
- Institute for Pharmaceutical Chemistry, Universität Wien, Austria
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13
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Virta P, Katajisto J, Niittymäki T, Lönnberg H. Solid-supported synthesis of oligomeric bioconjugates. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00704-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Okamoto A, Taiji T, Tainaka K, Saito I. Oligonucleotides containing 7-vinyl-7-deazaguanine as a facile strategy for expanding the functional diversity of DNA. Bioorg Med Chem Lett 2002; 12:1895-6. [PMID: 12113802 DOI: 10.1016/s0960-894x(02)00334-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A modified nucleobase 7-vinyl-7-deazaguanine ((V)G) produced adducts with maleimides through Diels-Alder cycloaddition under very mild conditions. By this method, post-synthetic modification to oligonucleotides with diverse functionality (carboxylic acid, pyrene, benzophenone, succinimidyl ester, nitroxide and biotin) was accomplished.
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Affiliation(s)
- Akimitsu Okamoto
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, SORST, Japan Science and Technology Corporation, Japan
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15
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Özdemir İ, Yiğit B, Çetinkaya B, Ülkü D, Tahir M, Arıcı C. Synthesis of a water-soluble carbene complex and its use as catalyst for the synthesis of 2,3-dimethylfuran. J Organomet Chem 2001. [DOI: 10.1016/s0022-328x(01)01029-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Hwang JT, Greenberg MM. Synthesis of 2'-modified oligodeoxynucleotides via on-column conjugation. J Org Chem 2001; 66:363-9. [PMID: 11429801 DOI: 10.1021/jo000917g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligodeoxynucleotides modified at the 2'-position of 2'-amino-2'-deoxyuridine or uridine were prepared in high yield and purity using phosphoramidites 2 and 3, respectively. Oligodeoxynucleotide conjugates were prepared on the solid-phase synthesis support following selective unmasking of the nucleophile incorporated in these phosphoramidites. Synthesis of oligodeoxynucleotides modified at the 2'-position of an internal nucleotide provides molecules that are complementary to those previously prepared via a similar approach using C5-substituted pyrimidines. The efficiency of functionalization of the 2'-O-alkylamino-uridine derived from 3 in a protected oligodeoxynucleotide was less susceptible to steric hindrance than the 2'-amino-2'-deoxyuridine in the same polymeric substrate. However, the greater reactivity of the 2'-O-alkylamine containing nucleotide gave rise to undesired acetamide formation resulting from nucleophilic attack on the 5'-terminal acetate in capped failure sequences. This problem was overcome by using 2,2,2-trimethylacetyl anhydride as a capping agent during the automated synthesis cycles. Finally, the efficiency of the photochemical unmasking of the support bound alkylamine on a 1 mumole scale was improved by using two 20 min photolysis cycles, coupled with removing reaction byproducts between cycles.
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Affiliation(s)
- J T Hwang
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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