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Meschaninova MI, Novopashina DS, Semikolenova OA, Silnikov VN, Venyaminova AG. Novel Convenient Approach to the Solid-Phase Synthesis of Oligonucleotide Conjugates. Molecules 2019; 24:E4266. [PMID: 31771111 PMCID: PMC6930482 DOI: 10.3390/molecules24234266] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/03/2023] Open
Abstract
A novel and convenient approach for the solid-phase 5'-functionalization of oligonucleotides is proposed in this article. The approach is based on the activation of free 5'-hydroxyl of polymer support-bound protected oligonucleotides by N,N'-disuccinimidyl carbonate followed by interaction with amino-containing ligands. Novel amino-containing derivatives of closo-dodecaborate, estrone, cholesterol, and α-tocopherol were specially prepared. A wide range of oligonucleotide conjugates bearing closo-dodecaborate, short peptide, pyrene, lipophilic residues (cholesterol, α-tocopherol, folate, estrone), aliphatic diamines, and propargylamine were synthesized and characterized to demonstrate the versatility of the approach. The developed method is suitable for the conjugate synthesis of oligonucleotides of different types (ribo-, deoxyribo-, 2'-O-methylribo-, and others).
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Affiliation(s)
- Mariya I. Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Olga A. Semikolenova
- Department of Natural Sciences, Novosibirsk State University, Pirogova str.2, Novosibirsk 630090, Russia;
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave.8, Novosibirsk 630090, Russia; (M.I.M.); (V.N.S.); (A.G.V.)
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Fonvielle M, Bouhss A, Hoareau C, Patin D, Mengin-Lecreulx D, Iannazzo L, Sakkas N, El Sagheer A, Brown T, Ethève-Quelquejeu M, Arthur M. Synthesis of Lipid-Carbohydrate-Peptidyl-RNA Conjugates to Explore the Limits Imposed by the Substrate Specificity of Cell Wall Enzymes on the Acquisition of Drug Resistance. Chemistry 2018; 24:14911-14915. [PMID: 30020544 DOI: 10.1002/chem.201802360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/16/2018] [Indexed: 01/10/2023]
Abstract
Conjugation of RNA with multiple partners to obtain mimics of complex biomolecules is limited by the identification of orthogonal reactions. Here, lipid-carbohydrate-peptidyl-RNA conjugates were obtained by post-functionalization reactions, solid-phase synthesis, and enzymatic steps, to generate molecules mimicking the substrates of FmhB, an essential peptidoglycan synthesis enzyme of Staphylococcus aureus. Mimics of Gly-tRNAGly and lipid intermediate II (undecaprenyl-diphospho-disaccharide-pentapeptide) were combined in a single "bi-substrate" inhibitor (IC50 =56 nm). The synthetic route was exploited to generate substrates and inhibitors containing d-lactate residue (d-Lac) instead of d-Ala at the C-terminus of the pentapeptide stem, a modification responsible for vancomycin resistance in the enterococci. The substitution impaired recognition of peptidoglycan precursors by FmhB. The associated fitness cost may account for limited dissemination of vancomycin resistance genes in S. aureus.
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Affiliation(s)
- Matthieu Fonvielle
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Present address: Laboratoire Structure-Activité des Biomolécules, Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Coralie Hoareau
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Affaf El Sagheer
- Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt.,Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Michel Arthur
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
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5
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Gvozdeva OV, Prassolov VS, Zenkova MA, Vlassov VV, Chernolovskaya EL. Silencing of Inducible Immunoproteasome Subunit Expression by Chemically Modified siRNA and shRNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:389-403. [PMID: 27351110 DOI: 10.1080/15257770.2016.1184275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Overexpression of inducible subunits of immunoproteasome is related to pathogenesis of some chronic diseases. Specific inhibition of the immunosubunits may be used for the treatment of these diseases and RNA interference is one of the potent methods used in this area. We designed 2'-O-methyl modified siRNAs with selectively protected nuclease-sensitive sites, which efficiently silence LMP2, LMP7, and MECL-1 genes expression. To provide stable long-lasting inhibition of target genes, short-hairpin RNAs (shRNA) expressed by lentiviral vectors were constructed. Our results demonstrated that chemically modified siRNAs inhibited the expression of target genes with similar efficiency or with efficiency exceeding that of corresponding shRNAs and provide silencing effect for 5 days.
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Affiliation(s)
- Olga V Gvozdeva
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk , Russia
| | | | - Marina A Zenkova
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk , Russia
| | - Valentin V Vlassov
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk , Russia
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Gvozdeva OV, Dovydenko IS, Venyaminova AG, Zenkova MA, Vlassov VV, Chernolovskaya EL. 42- and 63-bp anti-MDR1-siRNAs bearing 2'-OMe modifications in nuclease-sensitive sites induce specific and potent gene silencing. FEBS Lett 2014; 588:1037-43. [PMID: 24561194 DOI: 10.1016/j.febslet.2014.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 01/10/2023]
Abstract
DsRNAs longer than 30bp induce interferon response and global changes in gene expression profile in mammalians. 21bp siRNA and 25/27bp dsiRNA acting via RNA interference mechanism are used for specific gene silencing in this class of organisms. We designed selectively 2'-O-methyl-modified 42 and 63bp anti-MDR1-siRNAs that silence the expression of P-glycoprotein and restore the sensitivity of drug-resistant cancer cells to cytostatic more efficiently than canonical 21bp siRNAs. We also show that they act in a Dicer-independent mode and are devoid of immunostimulating properties. Our findings suggest that 42 and 63bp siRNAs could be used as potential therapeutics.
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Affiliation(s)
- Olga V Gvozdeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Iiya S Dovydenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Elena L Chernolovskaya
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Avenue, Novosibirsk 630090, Russia.
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Petrova NS, Chernikov IV, Meschaninova MI, Dovydenko IS, Venyaminova AG, Zenkova MA, Vlassov VV, Chernolovskaya EL. Carrier-free cellular uptake and the gene-silencing activity of the lipophilic siRNAs is strongly affected by the length of the linker between siRNA and lipophilic group. Nucleic Acids Res 2011; 40:2330-44. [PMID: 22080508 PMCID: PMC3299988 DOI: 10.1093/nar/gkr1002] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The conjugation of siRNA to molecules, which can be internalized into the cell via natural transport mechanisms, can result in the enhancement of siRNA cellular uptake. Herein, the carrier-free cellular uptake of nuclease-resistant anti-MDR1 siRNA equipped with lipophilic residues (cholesterol, lithocholic acid, oleyl alcohol and litocholic acid oleylamide) attached to the 5′-end of the sense strand via oligomethylene linker of various length was investigated. A convenient combination of H-phosphonate and phosphoramidite methods was developed for the synthesis of 5′-lipophilic conjugates of siRNAs. It was found that lipophilic siRNA are able to effectively penetrate into HEK293, HepG2 and KB-8-5 cancer cells when used in a micromolar concentration range. The efficiency of the uptake is dependent upon the type of lipophilic moiety, the length of the linker between the moiety and the siRNA and cell type. Among all the conjugates tested, the cholesterol-conjugated siRNAs with linkers containing from 6 to 10 carbon atoms demonstrate the optimal uptake and gene silencing properties: the shortening of the linker reduces the efficiency of the cellular uptake of siRNA conjugates, whereas the lengthening of the linker facilitates the uptake but retards the gene silencing effect and decreases the efficiency of the silencing.
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Affiliation(s)
- Natalya S Petrova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev ave., 8, Novosibirsk 630090, Russia
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