1
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Gorai A, Chaudhuri R, Mukhopadhyay TK, Datta A, Dash J. Thiazole Containing PNA Mimic Regulates c-MYC Gene Expression through DNA G-Quadruplex. Bioconjug Chem 2022; 33:1145-1155. [PMID: 35537180 DOI: 10.1021/acs.bioconjchem.2c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acids (PNAs), besides hybridizing to complementary DNA and RNAs, bind and stabilize DNA secondary structures. Herein, we illustrate the design and synthesis of PNA-like scaffolds by incorporating five-membered thiazole rings as modified bases instead of nucleobases and their subsequent effects on gene regulation by biophysical and in vitro assays. A thiazole-modified PNA trimer selectively recognizes c-MYC G-quadruplex (G4) DNA over other G4s and duplex DNA. It displays a high stabilization potential for the c-MYC G4 DNA and shows remarkable fluorescence enhancement with the c-MYC G4. It is flexible enough to bind at 5' and 3' ends as well as in the groove region of c-MYC G4. Furthermore, the PNA trimer easily permeates the cellular membrane and suppresses c-MYC mRNA expression in HeLa cells by targeting the promoter G4. This study illuminates modified PNAs as flexible molecular tools for selective targeting of noncanonical nucleic acids and modulating gene function.
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Affiliation(s)
- Ananta Gorai
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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2
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Wang F, Liu LS, Li P, Lau CH, Leung HM, Chin YR, Tin C, Lo PK. Cellular uptake, tissue penetration, biodistribution, and biosafety of threose nucleic acids: Assessing in vitro and in vivo delivery. Mater Today Bio 2022; 15:100299. [PMID: 35637854 PMCID: PMC9142632 DOI: 10.1016/j.mtbio.2022.100299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022]
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3
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Honcharenko D, Rocha CSJ, Lundin KE, Maity J, Milton S, Tedebark U, Murtola M, Honcharenko M, Slaitas A, Smith CIE, Zain R, Strömberg R. 2'- O-( N-(Aminoethyl)carbamoyl)methyl Modification Allows for Lower Phosphorothioate Content in Splice-Switching Oligonucleotides with Retained Activity. Nucleic Acid Ther 2022; 32:221-233. [PMID: 35238623 PMCID: PMC9221157 DOI: 10.1089/nat.2021.0086] [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] [Indexed: 11/23/2022] Open
Abstract
2′-O-(N-(Aminoethyl)carbamoyl)methyl (2′-O-AECM)-modified oligonucleotides (ONs) and their mixmers with 2′-O-methyl oligonucleotides (2′-OMe ONs) with phosphodiester linkers as well as with partial and full phosphorothioate (PS) inclusion were synthesized and functionally evaluated as splice-switching oligonucleotides in several different reporter cell lines originating from different tissues. This was enabled by first preparing the AECM-modified A, C, G and U, which required a different strategy for each building block. The AECM modification has previously been shown to provide high resistance to enzymatic degradation, even without PS linkages. It is therefore particularly interesting and unprecedented that the 2′-O-AECM ONs are shown to have efficient splice-switching activity even without inclusion of PS linkages and found to be as effective as 2′-OMe PS ONs. Importantly, the PS linkages can be partially included, without any significant reduction in splice-switching efficacy. This suggests that AECM modification has the potential to be used in balancing the PS content of ONs. Furthermore, conjugation of 2′-O-AECM ONs to an endosomal escape peptide significantly increased splice-switching suggesting that this effect could possibly be due to an increase in uptake of ON to the site of action.
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Affiliation(s)
- Dmytro Honcharenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cristina S J Rocha
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Jyotirmoy Maity
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Stefan Milton
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ulf Tedebark
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | | | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden.,Department of Clinical Genetics, Center for Rare Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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4
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Zhou Y, Zang C, Wang H, Li J, Cui Z, Li Q, Guo F, Yan Z, Wen X, Xi Z, Zhou C. 4'-C-Trifluoromethyl modified oligodeoxynucleotides: synthesis, biochemical studies, and cellular uptake properties. Org Biomol Chem 2020; 17:5550-5560. [PMID: 31112186 DOI: 10.1039/c9ob00765b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Herein, we report the synthesis of 4'-C-trifluoromethyl (4'-CF3) thymidine (T4'-CF3) and its incorporation into oligodeoxynucleotides (ODNs) through solid-supported DNA synthesis. The 4'-CF3 modification leads to a marginal effect on the deoxyribose conformation and a local helical structure perturbation for ODN/RNA duplexes. This type of modification slightly decreases the thermal stability of ODN/RNA duplexes (-1 °C/modification) and leads to improved nuclease resistance. Like the well-known phosphorothioate (PS) modification, heavy 4'-CF3 modifications enable direct cellular uptake of the modified ODNs without any delivery reagents. This work highlights that 4'-CF3 modified ODNs are promising candidates for antisense-based therapeutics, which will, in turn, inspire us to develop more potent modifications for antisense ODNs and siRNAs.
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Affiliation(s)
- Yifei Zhou
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.
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5
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Nawale GN, Bahadorikhalili S, Sengupta P, Kadekar S, Chatterjee S, Varghese OP. 4′-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading. Chem Commun (Camb) 2019; 55:9112-9115. [DOI: 10.1039/c9cc04141a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present synthesis, biochemical, biophysical and computational evaluation of 4′ gunanidino modified siRNA.
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Affiliation(s)
- Ganesh N. Nawale
- Translational Chemical Biology Laboratory
- Division of Polymer Chemistry
- Department of Chemistry-Ångström
- Uppsala University
- Uppsala
| | - Saeed Bahadorikhalili
- Translational Chemical Biology Laboratory
- Division of Polymer Chemistry
- Department of Chemistry-Ångström
- Uppsala University
- Uppsala
| | - Pallabi Sengupta
- Biomolecular NMR and Drug Design Laboratory
- Department of Biophysics
- Bose Institute
- Kolkata
- India
| | - Sandeep Kadekar
- Translational Chemical Biology Laboratory
- Division of Polymer Chemistry
- Department of Chemistry-Ångström
- Uppsala University
- Uppsala
| | - Subhrangsu Chatterjee
- Biomolecular NMR and Drug Design Laboratory
- Department of Biophysics
- Bose Institute
- Kolkata
- India
| | - Oommen P. Varghese
- Translational Chemical Biology Laboratory
- Division of Polymer Chemistry
- Department of Chemistry-Ångström
- Uppsala University
- Uppsala
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6
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Hagedorn PH, Persson R, Funder ED, Albæk N, Diemer SL, Hansen DJ, Møller MR, Papargyri N, Christiansen H, Hansen BR, Hansen HF, Jensen MA, Koch T. Locked nucleic acid: modality, diversity, and drug discovery. Drug Discov Today 2017; 23:101-114. [PMID: 28988994 DOI: 10.1016/j.drudis.2017.09.018] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/01/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with improved pharmacological properties in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity and potency, is widely used for this purpose. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide is a unique entity, and small structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.
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Affiliation(s)
- Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Robert Persson
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Erik D Funder
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Nanna Albæk
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Sanna L Diemer
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Dennis J Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Marianne R Møller
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Natalia Papargyri
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Christiansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Bo R Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Henrik F Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Mads A Jensen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark.
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7
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Biscans A, Bertrand JR, Dubois J, Rüger J, Vasseur JJ, Sczakiel G, Dupouy C, Debart F. Lipophilic 2′-O-Acetal Ester RNAs: Synthesis, Thermal Duplex Stability, Nuclease Resistance, Cellular Uptake, and siRNA Activity after Spontaneous Naked Delivery. Chembiochem 2016; 17:2054-2062. [DOI: 10.1002/cbic.201600317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Annabelle Biscans
- IBMM; UMR 5247 CNRS; Université Montpellier; ENSCM; Campus Triolet; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Jean-Rémi Bertrand
- UMR 8203 CNRS; Université Paris-Sud; Gustave Roussy; Université Paris-Saclay; 114 rue Edouard Vaillant 94805 Villejuif Cedex France
| | - Josephine Dubois
- Institut für Molekulare Medizin; Universitätsklinikum Schleswig-Holstein; Universität zu Lübeck; Ratzeburger Allee 160 23538 Lübeck Germany
| | - Jacqueline Rüger
- Institut für Molekulare Medizin; Universitätsklinikum Schleswig-Holstein; Universität zu Lübeck; Ratzeburger Allee 160 23538 Lübeck Germany
| | - Jean-Jacques Vasseur
- IBMM; UMR 5247 CNRS; Université Montpellier; ENSCM; Campus Triolet; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Georg Sczakiel
- Institut für Molekulare Medizin; Universitätsklinikum Schleswig-Holstein; Universität zu Lübeck; Ratzeburger Allee 160 23538 Lübeck Germany
| | - Christelle Dupouy
- IBMM; UMR 5247 CNRS; Université Montpellier; ENSCM; Campus Triolet; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Françoise Debart
- IBMM; UMR 5247 CNRS; Université Montpellier; ENSCM; Campus Triolet; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
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8
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Biscans A, Rouanet S, Bertrand JR, Vasseur JJ, Dupouy C, Debart F. Synthesis, binding, nuclease resistance and cellular uptake properties of 2'-O-acetalester-modified oligonucleotides containing cationic groups. Bioorg Med Chem 2015; 23:5360-8. [PMID: 26260340 DOI: 10.1016/j.bmc.2015.07.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 11/18/2022]
Abstract
We report on the synthesis and properties of oligonucleotides (ONs) with 2'-O-acetalester modifications containing cationic side chains in a prodrug-like approach. In the aim to improve cell penetration and nuclease resistance, various different amino- or guanidino-acetalester were grafted to 2'-OH of uridine and the corresponding phosphoramidites were incorporated into ONs. Introduction of 2'-O-(2-aminomethyl-2-ethyl)butyryloxymethyl (AMEBuOM) modification into 2'-OMe ONs leads to high resistance towards enzymatic degradation and to destabilization of duplexes with complementary RNA strand. Spontaneous uptake experiments of a twelve-mer containing ten 2'-O-AMEBuOM-U units into A673 cells showed moderate internalization of ON within the cells whereas substantial internalization of the corresponding lipophilic 2'-O-pivaloyloxymethyl ON was observed for the first time.
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Affiliation(s)
- Annabelle Biscans
- Department of Nucleic Acids, IBMM UMR 5247, CNRS-Université Montpellier-ENSCM, UM Campus Triolet, Place E. Bataillon, 34095 Montpellier Cedex 05, France
| | - Sonia Rouanet
- Department of Nucleic Acids, IBMM UMR 5247, CNRS-Université Montpellier-ENSCM, UM Campus Triolet, Place E. Bataillon, 34095 Montpellier Cedex 05, France
| | - Jean-Rémi Bertrand
- UMR 8203 CNRS, Université Paris-Saclay, Institut Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif Cedex, France
| | - Jean-Jacques Vasseur
- Department of Nucleic Acids, IBMM UMR 5247, CNRS-Université Montpellier-ENSCM, UM Campus Triolet, Place E. Bataillon, 34095 Montpellier Cedex 05, France
| | - Christelle Dupouy
- Department of Nucleic Acids, IBMM UMR 5247, CNRS-Université Montpellier-ENSCM, UM Campus Triolet, Place E. Bataillon, 34095 Montpellier Cedex 05, France.
| | - Françoise Debart
- Department of Nucleic Acids, IBMM UMR 5247, CNRS-Université Montpellier-ENSCM, UM Campus Triolet, Place E. Bataillon, 34095 Montpellier Cedex 05, France.
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9
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Brzezinska J, Markiewicz WT. Non-Nucleosidic Analogues of Polyaminonucleosides and Their Influence on Thermodynamic Properties of Derived Oligonucleotides. Molecules 2015; 20:12652-69. [PMID: 26184145 PMCID: PMC6332422 DOI: 10.3390/molecules200712652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 11/22/2022] Open
Abstract
The rationale for the synthesis of cationic modified nucleosides is higher expected nuclease resistance and potentially better cellular uptake due to an overall reduced negative charge based on internal charge compensation. Due to the ideal distance between cationic groups, polyamines are perfect counterions for oligodeoxyribonucleotides. We have synthesized non-nucleosidic analogues built from units that carry different diol structures instead of sugar residues and functionalized with polyamines. The non-nucleosidic analogues were attached as internal or 5′-terminal modifications in oligodeoxyribonucleotide strands. The thermodynamic studies of these polyaminooligonucleotide analogues revealed stabilizing or destabilizing effects that depend on the linker or polyamine used.
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Affiliation(s)
- Jolanta Brzezinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
| | - Wojciech T Markiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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10
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Guenther DC, Kumar P, Anderson BA, Hrdlicka PJ. C5-amino acid functionalized LNA: positively poised for antisense applications. Chem Commun (Camb) 2015; 50:9007-9. [PMID: 24983883 DOI: 10.1039/c4cc03623a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Incorporation of positively charged C5-amino acid functionalized LNA uridines into oligodeoxyribonucleotides (ONs) results in extraordinary RNA affinity, binding specificity and stability towards 3'-exonucleases.
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Affiliation(s)
- Dale C Guenther
- Department of Chemistry, University of Idaho, 875 Perimeter Drive MS2343, Moscow, ID 83844-2343, USA.
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11
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Shiraishi T, Nielsen PE. Cellular delivery of peptide nucleic acids (PNAs). Methods Mol Biol 2014; 1050:193-205. [PMID: 24297361 DOI: 10.1007/978-1-62703-553-8_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cellular delivery methods are a prerequisite for cellular studies with PNA. This chapter describes PNA cellular delivery using cell-penetrating peptide (CPP)-PNA conjugates and transfection of PNA-ligand conjugates mediated by cationic lipids. Furthermore, two endosomolytic procedures employing chloroquine treatment or photochemical internalization (PCI) for significantly improving PNA delivery efficacy are described.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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12
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Abramova TV, Belov SS, Tarasenko YV, Silnikov VN. Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics. Beilstein J Org Chem 2014; 10:1151-8. [PMID: 24991266 PMCID: PMC4077379 DOI: 10.3762/bjoc.10.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/23/2014] [Indexed: 12/14/2022] Open
Abstract
An efficient solid-phase-supported peptide synthesis (SPPS) of morpholinoglycine oligonucleotide (MorGly) mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits.
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Affiliation(s)
- Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Sergey S Belov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia ; Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia
| | - Yulia V Tarasenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
| | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrent'ev Ave, 8, Novosibirsk 630090, Russia
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13
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Uehara S, Hiura S, Higashida R, Oka N, Wada T. Solid-phase synthesis of P-boronated oligonucleotides by the H-boranophosphonate method. J Org Chem 2014; 79:3465-72. [PMID: 24679151 DOI: 10.1021/jo500185b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recently, P-boronated oligonucleotides have been attracting much attention as potential therapeutic oligonucleotides. In this study, we developed H-boranophosphonate oligonucleotide bearing a borano group and hydrogen atom on the internucleotidic phosphorus and demonstrated that this novel P-boronated oligonucleotide is a versatile precursor to various P-boronated oligonucleotides such as boranophosphate, boranophosphorothioate, and boranophosphoramidate. The method was also applicable to the synthesis of a locked nucleic acid-modified boranophosphate oligonucleotide, which exhibited a dramatically enhanced affinity to complementary oligonucleotides.
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Affiliation(s)
- Sho Uehara
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Bioscience Building 702, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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14
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Koch T, Shim I, Lindow M, Ørum H, Bohr HG. Quantum mechanical studies of DNA and LNA. Nucleic Acid Ther 2014; 24:139-48. [PMID: 24491259 DOI: 10.1089/nat.2013.0465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Quantum mechanical (QM) methodology has been employed to study the structure activity relations of DNA and locked nucleic acid (LNA). The QM calculations provide the basis for construction of molecular structure and electrostatic surface potentials from molecular orbitals. The topologies of the electrostatic potentials were compared among model oligonucleotides, and it was observed that small structural modifications induce global changes in the molecular structure and surface potentials. Since ligand structure and electrostatic potential complementarity with a receptor is a determinant for the bonding pattern between molecules, minor chemical modifications may have profound changes in the interaction profiles of oligonucleotides, possibly leading to changes in pharmacological properties. The QM modeling data can be used to understand earlier observations of antisense oligonucleotide properties, that is, the observation that small structural changes in oligonucleotide composition may lead to dramatic shifts in phenotypes. These observations should be taken into account in future oligonucleotide drug discovery, and by focusing more on non RNA target interactions it should be possible to utilize the exhibited property diversity of oligonucleotides to produce improved antisense drugs.
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15
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Synthesis, physicochemical and biochemical studies of anti-IRS-1 oligonucleotides containing carborane and/or metallacarborane modification. J Organomet Chem 2013. [DOI: 10.1016/j.jorganchem.2013.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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He J, Kauffman WB, Fuselier T, Naveen SK, Voss TG, Hristova K, Wimley WC. Direct cytosolic delivery of polar cargo to cells by spontaneous membrane-translocating peptides. J Biol Chem 2013; 288:29974-86. [PMID: 23983125 DOI: 10.1074/jbc.m113.488312] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Direct cellular entry of potentially useful polar compounds into cells is prevented by the hydrophobic barrier of the membrane. Toward circumventing this barrier, we used high throughput screening to identify a family of peptides that carry membrane-impermeant cargos across synthetic membranes. Here we characterize the plasma membrane translocation of these peptides with polar cargos under a variety of conditions. The spontaneous membrane-translocating peptides (SMTPs) delivered the zwitterionic, membrane-impermeant dye tetramethylrhodamine (TAMRA) into cells even when the conditions were not permissive for endocytosis. They also delivered the larger, anionic membrane-impermeant dye Alexa Fluor 546 but did not deliver a quantum dot nanoparticle. Under all conditions, the SMTP-cargo filled the cytoplasm with a diffuse, non-punctate fluorescence that was partially excluded from the nucleus. D-amino acid peptides behaved identically in vitro, ruling out proteolysis as an important factor in the diffuse cellular distribution. Thus, cytosolic delivery of SMTP-cargo conjugates is dominated by direct membrane translocation. This is in sharp contrast to Arg9-TAMRA, a representative highly cationic, cell-penetrating peptide, which entered cells only when endocytosis was permitted. Arg9-TAMRA triggered large scale endocytosis and did not appreciably escape the endosomal compartments in the 1-h timescales we studied. When injected into mice, SMTP-TAMRA conjugates were found in many tissues even after 2 h. Unconjugated TAMRA was rapidly cleared and did not become systemically distributed. SMTPs are a platform that could improve delivery of many polar compounds to cells, in the laboratory or in the clinic, including those that would otherwise be rejected as drugs because they are membrane-impermeant.
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Affiliation(s)
- Jing He
- From the Departments of Biochemistry and
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17
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Design and chemical modification of synthetic short shRNAs as potent RNAi triggers. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 942:279-90. [PMID: 23027057 DOI: 10.1007/978-1-62703-119-6_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Synthetic shRNAs that are too short to be Dicer substrates (short shRNAs or sshRNAs) can be highly potent RNAi effectors when properly designed, with activities similar to or more potent than the more commonly used siRNAs targeting the same sequences. sshRNAs can be designed in two possible orientations: left- or right-hand loop, designated L-sshRNAs and R-sshRNAs, respectively. Because L- and R-sshRNAs are processed by the RNAi machinery in different ways, optimal designs for the two formats diverge in several key aspects. Here, we describe the principles of design and chemical modification of highly effective L- and R-sshRNAs.
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18
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Lietard J, Leumann CJ. Synthesis, pairing, and cellular uptake properties of C(6')-functionalized tricyclo-DNA. J Org Chem 2012; 77:4566-77. [PMID: 22551389 DOI: 10.1021/jo300648u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Tricyclo-DNA (tc-DNA) is a promising candidate for oligonucleotide-based therapeutic applications exhibiting increased affinity to RNA and increased resistance to nucleases. However, as many other oligonucleotide analogs, tc-DNA does not readily cross cell membranes. We wished to address this issue by preparing a prodrug of tc-DNA containing a metabolically labile group at C(6') that promotes cellular uptake. Two monomeric nucleoside building blocks bearing an ester function at C(6') (tc(ee)-T and tc(hd)-T) were synthesized starting from a known C(6') functionalized bicyclic sugar unit to which the cyclopropane ring was introduced via carbene addition. NIS-mediated nucleosidation of the corresponding glycal with in situ persilylated thymine afforded the β-iodonucleoside exclusively that was dehalogenated via radical reduction. Diversity in the ester function was obtained by hydrolysis and reesterification. The two nucleosides were subsequently incorporated into DNA or tc-DNA by standard phosphoramidite chemistry. The reactivity of the ester function during oligonucleotide deprotection was explored and the corresponding C(6') amide, carboxylic acid, or unchanged ester functions were obtained, depending on the deprotection conditions. Compared to unmodified DNA, these tc-DNA derivatives increased the stability of duplexes investigated with ΔT(m)/mod of +0.4 to +2.0 °C. The only destabilizing residue was tc(hd)-T, most likely due to self-aggregation of the lipophilic side chains in the single stranded oligonucleotide. A decamer containing five tc(hd)-T residues was readily taken up by HeLa and HEK 293T cells without the use of a transfection agent.
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Affiliation(s)
- Jory Lietard
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
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19
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Enzymatic polymerisation involving 2'-amino-LNA nucleotides. Bioorg Med Chem Lett 2012; 22:3522-6. [PMID: 22503454 DOI: 10.1016/j.bmcl.2012.03.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 03/19/2012] [Accepted: 03/21/2012] [Indexed: 11/21/2022]
Abstract
The triphosphate of the thymine derivative of 2'-amino-LNA (2'-amino-LNA-TTP) was synthesised and found to be a good substrate for Phusion® HF DNA polymerase, allowing enzymatic synthesis of modified DNA encoded by an unmodified template. To complement this, 2'-amino-LNA-T phosphoramidites were incorporated into DNA oligonucleotides which were used as templates for enzymatic synthesis of unmodified DNA using either KOD, KOD XL or Phusion polymerases. 2'-Amino-LNA-T in the template and 2'-amino-LNA-TTP as a substrate both decreased reaction rate and yield compared to unmodified DNA, especially for sequences with multiple 2'-amino-LNA-T nucleotides.
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20
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Gore KR, Nawale GN, Harikrishna S, Chittoor VG, Pandey SK, Höbartner C, Patankar S, Pradeepkumar PI. Synthesis, gene silencing, and molecular modeling studies of 4'-C-aminomethyl-2'-O-methyl modified small interfering RNAs. J Org Chem 2012; 77:3233-45. [PMID: 22372696 DOI: 10.1021/jo202666m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The linear syntheses of 4'-C-aminomethyl-2'-O-methyl uridine and cytidine nucleoside phosphoramidites were achieved using glucose as the starting material. The modified RNA building blocks were incorporated into small interfering RNAs (siRNAs) by employing solid phase RNA synthesis. Thermal melting studies showed that the modified siRNA duplexes exhibited slightly lower T(m) (∼1 °C/modification) compared to the unmodified duplex. Molecular dynamics simulations revealed that the 4'-C-aminomethyl-2'-O-methyl modified nucleotides adopt South-type conformation in a siRNA duplex, thereby altering the stacking and hydrogen-bonding interactions. These modified siRNAs were also evaluated for their gene silencing efficiency in HeLa cells using a luciferase-based reporter assay. The results indicate that the modifications are well tolerated in various positions of the passenger strand and at the 3' end of the guide strand but are less tolerated in the seed region of the guide strand. The modified siRNAs exhibited prolonged stability in human serum compared to unmodified siRNA. This work has implications for the use of 4'-C-aminomethyl-2'-O-methyl modified nucleotides to overcome some of the challenges associated with the therapeutic utilities of siRNAs.
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Affiliation(s)
- Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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21
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Abstract
The chemistry of the oligonucleotide backbone is crucial to obtaining high activity in vivo in exon skipping applications. Apart from the ability to bind strongly and sequence-specifically to pre-mRNA targets, the type of backbone also influences cell delivery, in vivo pharmacology, bio-distribution, toxicology, and ultimately the therapeutic use in humans. Reviewed here are classes of oligonucleotide commonly used for exon skipping applications, namely negatively charged backbones typified by RNA analogues having 2'-O-substitution and a phosphorothioate linkage and charge-neutral backbones such as PNA and PMO. Also discussed are peptide conjugates of PNA and PMO that enhance cellular and in vivo delivery and their potential for drug development. Finally, the prospects for development of other analogue types in exon skipping applications are outlined.
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22
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Lietard J, Ittig D, Leumann CJ. Synthesis, binding and cellular uptake properties of oligodeoxynucleotides containing cationic bicyclo-thymidine residues. Bioorg Med Chem 2011; 19:5869-75. [PMID: 21889348 DOI: 10.1016/j.bmc.2011.08.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 07/29/2011] [Accepted: 08/09/2011] [Indexed: 11/27/2022]
Abstract
The synthesis and incorporation into oligodeoxynucleotides of two novel derivatives of bicyclothymidine carrying a cationic diaminopropyl or lysine unit in the C(6')-β position is described. Compared to unmodified DNA these oligonucleotides show T(m)-neutral behavior when paired against complementary DNA and are destabilizing when paired against RNA. Unaided uptake experiments of a decamer containing five lys-bcT units into HeLa and HEK293T cells showed substantial internalization with mostly cytosolic distribution which was not observed in the case of an unmodified control oligonucleotide.
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Affiliation(s)
- Jory Lietard
- Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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23
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Enhanced cellular delivery of cell-penetrating peptide-peptide nucleic acid conjugates by photochemical internalization. Methods Mol Biol 2011. [PMID: 21053145 DOI: 10.1007/978-1-60761-919-2_28] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Cell-penetrating peptides (CPPs) have been widely used for a cellular delivery of biologically relevant cargoes including antisense peptide nucleic acids (PNAs). Although chemical conjugation of PNA to a variety of CPPs significantly improves the cellular uptake of the PNAs, bioavailability (antisense activity) is still limited by endocytotic entrapment. We have shown that this low bioavailability can be greatly improved by combining CPP-PNA conjugate administration with a photochemical internalization technique using photosensitizers such as aluminum phthalocyanine (AlPcS(2a)) or tetraphenylporphyrin tetrasulfonic acid (TPPS). Cellular uptake of the PNA conjugates were evaluated by using a sensitive cellular method with HeLa pLuc705 cells based on the splicing correction of luciferase gene by targeting antisense oligonucleotides to a cryptic splice site of the mutated luciferase gene. The cellular efficacy of CPP conjugates were evaluated by measuring luciferase activity as a result of splicing correction and was also confirmed by RT-PCR analysis of luciferase pre-mRNA.
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24
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Meyer A, Pourceau G, Vasseur JJ, Morvan F. 5'-Bis-conjugation of oligonucleotides by amidative oxidation and click chemistry. J Org Chem 2011; 75:6689-92. [PMID: 20795720 DOI: 10.1021/jo101134z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A pent-4-ynyl tert-butyl N,N-diisopropyl phosphoramidite was coupled at the 5'-end of oligonucleotides to give a phosphite triester linkage, which forms an H-phosphonate diester linkage during treatment with dichloroacetic acid. Then an amidative oxidation with CCl(4) in the presence of an amine and a 1,3-dipolar cycloaddition with an azide under copper(I) catalysis afforded the bis-conjugated oligonucleotides with high efficiency. The introduction of a bromoalkyl group as a precursor of azidoalkyl by amidative oxidation allowed the performance of two selective 1,3-dipolar cycloadditions.
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Affiliation(s)
- Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS Université Montpellier 1, Université Montpellier 2, CC1704, Place E. Bataillon, 34095 Montpellier Cedex 5, France
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25
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Improved cellular uptake of antisense peptide nucleic acids by conjugation to a cell-penetrating peptide and a lipid domain. Methods Mol Biol 2011; 751:209-21. [PMID: 21674333 DOI: 10.1007/978-1-61779-151-2_13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unaided cellular uptake of RNA interference agents such as antisense oligonucleotides and siRNA is extremely poor, and in vivo bioavailability is also limited. Thus, effective delivery strategies for such potential drugs are in high demand. Recently, a novel approach using a class of short cationic peptides known as cell-penetrating peptides (CPPs) is attracting wide attention for a variety of biologically active molecules. CPP-mediated delivery is typically based on the covalent conjugation of the (therapeutic) cargo to CPPs, and is particularly relevant for the delivery of noncharged RNA interference agents such as peptide nucleic acids (PNAs) and morpholino oligomers. Although chemical conjugation to a variety of CPPs significantly improves the cellular uptake of PNAs, the bioavailability (and hence antisense activity) of CPP-PNA -conjugates is still highly limited by endocytotic entrapment. We have found, however, that this low -bioavailability can be significantly improved by chemical conjugation to a lipid domain ("Lip," such as a fatty acid), thereby creating "CatLip"-conjugates. The cellular uptake of these conjugates is conveniently evaluated using a sensitive cellular assay system based on a splicing correction of a mutated luciferase gene in HeLa pLuc705 cells by targeting antisense oligonucleotides to a cryptic splice site. Further improvement in the delivery of CatLip-PNA conjugates is achieved by using auxiliary agents/treatments (e.g., chloroquine, calcium ions, or photosensitizers) to induce endosomal disruption.
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26
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Park SM, Nam SJ, Jeong HS, Kim WJ, Kim BH. The effects of the 4-(4-Methylpiperazine)phenyl group on nucleosides and oligonucleotides: cellular delivery, detection, and stability. Chem Asian J 2010; 6:487-92. [PMID: 21254426 DOI: 10.1002/asia.201000574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Indexed: 11/11/2022]
Abstract
As drug candidates, one promising way to improve the cellular delivery efficacy of oligonucleotides is to introduce a cationic group. By introducing a cationic moiety into the oligonucleotide structure, they become capable of approaching the cell surface and also of crossing the cellular membrane. In an effort to develop cell-permeable oligonucleotides, we examined the piperazinephenyl-bearing 2'-deoxyuridine ((PP)U), which can be not only cationic but also fluorescent as a cationic monomer for cationic oligonucleotides. Several modified DNA oligonucleotides with different numbers of (PP)U building blocks were synthesized and evaluated for the effect on thermal stability and conformation by the introduction of (PP)U. The cellular delivery of modified oligonucleotides was different depending on the number of (PP)U building blocks. Furthermore, these (PP)U-modified oligonucleotides had sufficient fluorescence that we were able to identify the delivery results without the use of conventional fluorescent tags. They were predominantly localized in the cell cytoplasm. In addition, they were stable enough after 3 hours in the presence of nuclease. These results showed that a piperazinephenyl moiety that is conjugated with nucleobase is able to deliver and detect the oligonucleotides, which suggests that this concept of 'dual-function oligonucleotides' might be utilized in diagnostics, therapeutics, and as a convenient biological tool for probing the activity of oligonucleotides inside cells.
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Affiliation(s)
- Sun Min Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Republic of Korea
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27
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Johannsen MW, Crispino L, Wamberg MC, Kalra N, Wengel J. Amino acids attached to 2'-amino-LNA: synthesis and excellent duplex stability. Org Biomol Chem 2010; 9:243-52. [PMID: 21049102 DOI: 10.1039/c0ob00532k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of 2'-amino-LNA (the 2'-amino derivative of locked nucleic acid) has opened up a number of exciting possibilities with respect to modified nucleic acids. While maintaining the excellent duplex stability inferred by LNA-type oligonucleotides, the nitrogen in the 2'-position of 2'-amino-LNA monomers provides an excellent handle for functionalisation. Herein, the synthesis of amino acid functionalised 2'-amino-LNA derivatives is described. Following ON synthesis, a glycyl unit attached to the N2'-position of 2'-amino-LNA monomers was further acylated with a variety of amino acids. On binding to DNA/RNA complements, the modified ONs induce a marked increase in thermal stability, which is particularly apparent in a buffer system with a low salt concentration. The increase in thermal stability is thought to be caused, at least in part, by decreased electrostatic repulsion between the negatively charged phosphate backbones when positively charged amino acid residues are appended. Upon incorporation of more than one 2'-amino-LNA modification, the effects are found to be nearly additive. For comparison, 2'-amino-LNA derivatives modified with uncharged groups have been synthesised and their effect on duplex thermal stability likewise investigated.
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Affiliation(s)
- Marie W Johannsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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28
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Meyer A, Spinelli N, Dumy P, Vasseur JJ, Morvan F, Defrancq E. Oligonucleotide sequential bis-conjugation via click-oxime and click-Huisgen procedures. J Org Chem 2010; 75:3927-30. [PMID: 20443615 DOI: 10.1021/jo100599m] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel procedure has been developed for the bis-conjugation of oligonucleotides using CuAAC (click-H) and oxime (click-O) tethering strategies. Oligonucleotides bearing a 5'-alkyne function and a 3'-aldehyde precursor were synthesized and were bis-conjugated with various reporters including azido carbohydrate or fluorescent dye and aminooxy peptide or carbohydrate. Versatility of the method was demonstrated by performing click-O prior to click-H and vice versa. Interestingly, when click-O is achieved prior to click-H, no purification is required in between, allowing a sequential one-pot protocol.
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Affiliation(s)
- Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS Université Montpellier 1, 34095 Montpellier Cedex 5, France
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29
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Brown SD, Graham D. Conjugation of an oligonucleotide to Tat, a cell-penetrating peptide, via click chemistry. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.07.101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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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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31
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Morvan F, Debart F, Vasseur JJ. From anionic to cationic alpha-anomeric oligodeoxynucleotides. Chem Biodivers 2010; 7:494-535. [PMID: 20232324 DOI: 10.1002/cbdv.200900220] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université Montpellier 1 and Université Montpellier 2, Place Eugène Bataillon, CC1704, FR-34095 Montpellier cedex 5, France
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32
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Ming X, Alam MR, Fisher M, Yan Y, Chen X, Juliano RL. Intracellular delivery of an antisense oligonucleotide via endocytosis of a G protein-coupled receptor. Nucleic Acids Res 2010; 38:6567-76. [PMID: 20551131 PMCID: PMC2965246 DOI: 10.1093/nar/gkq534] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gastrin-releasing peptide receptor (GRPR), a member of the G protein-coupled receptor superfamily, has been utilized for receptor-mediated targeting of imaging and therapeutic agents; here we extend its use to oligonucleotide delivery. A splice-shifting antisense oligonucleotide was conjugated to a bombesin (BBN) peptide, and its intracellular delivery was tested in GRPR expressing PC3 cells stably transfected with a luciferase gene interrupted by an abnormally spliced intron. The BBN-conjugate produced significantly higher luciferase expression compared to unmodified oligonucleotide, and this increase was reversed by excess BBN peptide. Kinetic studies revealed a combination of saturable, receptor-mediated endocytosis and non-saturable pinocytosis for uptake of the conjugate. The Km value for saturable uptake was similar to the EC50 value for the pharmacological response, indicating that receptor-mediated endocytosis was a primary contributor to the response. Use of pharmacological and molecular inhibitors of endocytosis showed that the conjugate utilized a clathrin-, actin- and dynamin-dependent pathway to enter PC3 cells. The BBN-conjugate partially localized in endomembrane vesicles that were associated with Rab7 or Rab9, demonstrating that it was transported to late endosomes and the trans-golgi network. These observations suggest that the BBN-oligonucleotide conjugate enters cells via a process of GRPR mediated endocytosis followed by trafficking to deep endomembrane compartments.
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Affiliation(s)
- Xin Ming
- Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
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33
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Ge Q, Dallas A, Ilves H, Shorenstein J, Behlke MA, Johnston BH. Effects of chemical modification on the potency, serum stability, and immunostimulatory properties of short shRNAs. RNA (NEW YORK, N.Y.) 2010; 16:118-30. [PMID: 19948766 PMCID: PMC2802022 DOI: 10.1261/rna.1901810] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 10/16/2009] [Indexed: 05/23/2023]
Abstract
Small hairpin RNAs (shRNAs) with 19-base-pair, or shorter, stems (short shRNAs [sshRNAs]) have been found to constitute a class whose mechanism of action appears to be distinct from that of small interfering RNAs (siRNAs) or longer shRNAs. These sshRNAs can be as active as canonical siRNAs or longer shRNAs. Their activity is affected by whether the antisense strand is positioned 5' or 3' to the loop (L or R sshRNAs, respectively). Dicer seems not to be involved in the processing of sshRNAs, although the mechanism of target gene suppression by these hairpins is through Ago2-mediated mRNA cleavage. In this study, the effects of chemical modifications on the potency, serum stability, and innate immune response of sshRNAs were investigated. Deoxynucleotide substitution and 2'-O-methyl (2'-OMe) modification in the sense strand and loop did not affect silencing activity, but, unlike with siRNAs, when placed in the antisense strand these modifications were detrimental. Conjugation with bulky groups at the 5'-end of L sshRNAs or 3'-end of R sshRNAs had a negative impact on the potency. Unmodified sshRNAs in dimer form or with blunt ends were immunostimulatory. Some modifications such as 3'-end conjugation and phosphorothioate linkages on the backbone of the sshRNAs could also induce inflammatory cytokine production. However, 2'-OMe substitution of sshRNAs abrogated the innate immune response and improved the serum stability of the hairpins.
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Affiliation(s)
- Qing Ge
- SomaGenics, Inc., Santa Cruz, California 95060, USA.
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34
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Ge D, Wu D, Wang Z, Shi W, Wu T, Zhang A, Hong S, Wang J, Zhang Y, Ren L. Cellular Uptake Mechanism of Molecular Umbrella. Bioconjug Chem 2009; 20:2311-6. [DOI: 10.1021/bc9003074] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dongtao Ge
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Dewang Wu
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Zuyong Wang
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Wei Shi
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Ting Wu
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Aifeng Zhang
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Shimin Hong
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Jun Wang
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Ye Zhang
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
| | - Lei Ren
- Department of Biomaterials/Biomedical Engineering Research Center, College of Materials, State Key Laboratory for Physical Chemistry of Solid Surfaces, and Department of Preclinical Medicine, Medical College, Xiamen University, Xiamen 361005, China
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35
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Murat P, Spinelli N, Dumy P, Defrancq E. Efficient conjugation of oligonucleotides through aromatic oxime formation. Bioorg Med Chem Lett 2009; 19:6534-7. [PMID: 19857965 DOI: 10.1016/j.bmcl.2009.10.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 10/09/2009] [Accepted: 10/10/2009] [Indexed: 11/16/2022]
Abstract
The present work reports on the preparation of oligonucleotide conjugates via the formation of aromatic oxime linkage. The conjugation consists in the reaction between the oligonucleotide derivatized at 5'-extremity with a benzaldehyde moiety and an aminooxy reporter group. The conjugation was found highly efficient and was extended for the conjugation of phosphorothioate oligonucleotide. In addition, the stability of the so-formed oxime conjugate was investigated.
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Affiliation(s)
- Pierre Murat
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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36
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Luisier S, Leumann CJ. Screening the structural and functional properties of bicyclo-DNA: bc(ox)-DNA. Chembiochem 2009; 9:2244-53. [PMID: 18756553 DOI: 10.1002/cbic.200800322] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The synthesis of two novel pyrimidine bicyclonucleosides (bc(ox)-nucleosides) has been accomplished. These bicyclonucleosides each carry a lipophilic benzyloxime substituent on the carbocyclic ring and show improved conformational similarity to 2'-deoxyribonucleosides as shown by their X-ray structures. The thymine-containing bc(ox)-nucleoside was converted into the corresponding phosphoramidite building block and incorporated into oligodeoxyribonucleotides by standard phosphoramidite chemistry. T(m) data with complementary RNA and DNA were measured and compared to corresponding cases of natural and unfunctionalized bc-DNA. It was found that single incorporations of bc(ox) residues destabilize duplexes by roughly 5 degrees C per modification. The destabilization was found to be due to the oxime substituent and not to the bicyclic scaffold itself. No significant alteration of the base-pairing selectivity as a function of the modification was observed. With RNA (but not with DNA) as a complement the relative thermal destabilization of bc(ox)-oligothymidylates was gradually reduced and converted into a stabilizing interaction with increasing numbers of consecutive modifications. While no cellular uptake of bc(ox)-oligonucleotides into HeLa cells occurred without transfecting agents, a significant increase in the transfection rate relative to unmodified DNA was observed in complexation with lipofectamine.
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Affiliation(s)
- Samuel Luisier
- Department of Chemistry and Biochemistry, University of Bern, Switzerland
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37
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Abstract
Several strategies based on synthetic oligonucleotides (ON) have been proposed to control gene expression. As for most biomolecules, however, delivery has remained a major roadblock for in vivo applications. Conjugation of steric-block neutral DNA mimics such as peptide nucleic acids (PNA) or phosphorodiamidate morpholino oligonucleotides (PMO) to cell penetrating peptides (CPP) has recently been proposed as a new delivery strategy. It is particularly suitable to interfere sequence-specifically with pre-mRNA splicing thus offering various applications in fundamental research and in therapeutics. The chemical synthesis of these CPP conjugates as well as methodologies to monitor their cellular uptake and their efficiency in a reliable and easy to implement assay of splicing correction will be described.
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38
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Steven V, Graham D. Oligonucleotide conjugation to a cell-penetrating (TAT) peptide by Diels-Alder cycloaddition. Org Biomol Chem 2008; 6:3781-7. [PMID: 18843408 DOI: 10.1039/b807843b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Modifed oligonucleotides are routinely employed as analytical probes for use in diagnostics, e.g. in the examination of specific RNA sequences for infectious diseases, however, a major limiting factor in oligonucleotide-based diagnostics is poor cellular uptake of naked oligonucleotides. This problem can be overcome by covalent attachment of a so-called 'cell-penetrating peptide' to form an oligonucleotide peptide conjugate. Stepwise solid phase synthesis of such a conjugate is difficult and expensive due to the conflicting chemistries of oligonucleotides and peptides. A simple approach to overcome this is post-synthetic conjugation. Diels-Alder cycloaddition is an attractive methodology for oligonucleotide peptide conjugation; the reaction is fast, chemoselective and the reaction rate is greatly enhanced in aqueous media - ideal conditions for biological moieties. An oligodeoxyribonucleotide sequence has been derivatised with a series of dienes at the 5'-terminus, using a series of unique dienyl-modified phosphoramidites, and investigation into the effect of diene type on the efficiency of conjugation, using Diels-Alder cycloaddition with a maleimido-derivatised cell-penetrating (TAT) peptide, has been performed. This led to the observation that the optimal diene for conjugation was cyclohexadiene, allowing conjugation of oligodeoxyribonucleotides to a cell-penetrating peptide by Diels-Alder cycloaddition for the first time.
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Affiliation(s)
- Victoria Steven
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK
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Abes R, Arzumanov A, Moulton H, Abes S, Ivanova G, Gait MJ, Iversen P, Lebleu B. Arginine-rich cell penetrating peptides: design, structure-activity, and applications to alter pre-mRNA splicing by steric-block oligonucleotides. J Pept Sci 2008; 14:455-60. [PMID: 18236382 DOI: 10.1002/psc.979] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rerouting the splicing machinery with steric-block oligonucleotides (ON) might lead to new therapeutic strategies in the treatment of diseases such as beta-thalassemia, Duchenne muscular dystrophy, or cancers. Interfering with splicing requires the sequence-specific and stable hybridization of RNase H-incompetent ON as peptide nucleic acids (PNA) or phosphorodiamidate morpholino oligomers (PMO). Unfortunately, these uncharged DNA mimics are poorly taken up by most cell types and conventional delivery strategies that rely on electrostatic interaction do not apply. Likewise, conjugation to cell penetrating peptides (CPPs) as Tat, Arg9, Lys8, or Pen leads to poor splicing correction efficiency at low concentration essentially because PNA- and PMO-CPP conjugates remain entrapped within endocytotic vesicles. Recently, we have designed an arginine-rich peptide (R-Ahx-R)4 (with Ahx for aminohexanoic acid) and an arginine-tailed Penetratin derivative which allow sequence-specific and efficient splicing correction at low concentration in the absence of endosomolytic agents. Both CPPs are undergoing structure-activity relationship studies for further optimization as steric-block ON delivery vectors.
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Affiliation(s)
- R Abes
- UMR 5235 CNRS, Université Montpellier 2, Place Eugene Bataillon, 34095 Montpellier cedex 5, France
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Bobkov GV, Mikhailov SN, Van Aerschot A, Herdewijn P. Phosphoramidite building blocks for efficient incorporation of 2′-O-aminoethoxy(and propoxy)methyl nucleosides into oligonucleotides. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Oligonucleotide-polyamine conjugates: influence of length and position of 2'-attached polyamines on duplex stability and antisense effect. Eur J Med Chem 2008; 44:670-7. [PMID: 18617292 DOI: 10.1016/j.ejmech.2008.05.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 04/15/2008] [Accepted: 05/19/2008] [Indexed: 11/22/2022]
Abstract
Tethering cationic ligands to oligonucleotides results in zwitterionic molecules with often improved target affinity and better cell membrane permeation. Due to the ideal distance between cationic groups, polyamines are perfect counter ions for oligonucleotides. Using an easy and versatile procedure for attaching ligands to the 2'-position, polyamines were conjugated to distinct terminal and internal positions of oligonucleotides. With polyamines attached to terminal nucleosides, the affinity to complementary DNA or RNA strands increased with growing number of cationic amines. Tethering polyamines to an internal nucleoside of wild type DNA oligonucleotides resulted in a considerable decrease in duplex stability, but in phosphorothioates, no significant decrease was detected. Conjugates exhibited progressively higher target downregulation ability with increasing polyamine chain length in a human melanoma cell culture assay.
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Oligonucleotide antiviral therapeutics: antisense and RNA interference for highly pathogenic RNA viruses. Antiviral Res 2008; 78:26-36. [PMID: 18258313 PMCID: PMC7114189 DOI: 10.1016/j.antiviral.2007.12.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 12/05/2007] [Accepted: 12/06/2007] [Indexed: 11/21/2022]
Abstract
RNA viruses are a significant source of morbidity and mortality in humans every year. Additionally, the potential use of these viruses in acts of bioterrorism poses a threat to national security. Given the paucity of vaccines or postexposure therapeutics for many highly pathogenic RNA viruses, novel treatments are badly needed. Sequence-based drug design, under development for almost 20 years, is proving effective in animal models and has moved into clinical trials. Important advances in the field include the characterization of RNA interference in mammalian cells and chemical modifications that can dramatically increase the in vivo stability of therapeutic oligonucleotides. Antisense strategies utilize single-stranded DNA oligonucleotides that inhibit protein production by mediating the catalytic degradation of target mRNA, or by binding to sites on mRNA essential for translation. Double-stranded RNA oligonucleotides, known as short-interfering RNAs (siRNAs), also mediate the catalytic degradation of complementary mRNAs. As RNA virus infection is predicated on the delivery, replication, and translation of viral RNA, these pathogens present an obvious target for the rapidly advancing field of sequence-specific therapeutics. Antisense oligonucleotides or siRNAs can be designed to target the viral RNA genome or viral transcripts. This article reviews current knowledge on therapeutic applications of antisense and RNA interference for highly pathogenic RNA viral infections.
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Coward JK, McGuire JJ. Mechanism‐Based Inhibitors of Folylpoly‐γ‐Glutamate Synthetase and γ‐Glutamyl Hydrolase: Control of Folylpoly‐γ‐Glutamate Homeostasis as a Drug Target. FOLIC ACID AND FOLATES 2008; 79:347-73. [DOI: 10.1016/s0083-6729(08)00412-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Abstract
Oligonucleotides can in a variety of ways inhibit gene expression by interfering with translation. Oligonucleotides that are complementary to a target mRNA, antisense oligonucleotides, can prevent translation either by cleaving the target or by physically blocking the process. Additionally, oligonucleotides can correct the undesired splicing of pre-mRNA. RNA interference using double-stranded oligoribonucleotides also results in cleavage of the target mRNA. Catalytically competent ribozymes and DNAzymes can have the same effect. Even with no RNA as target, oligonucleotides can be selected as aptamers to bind to any protein to inhibit its activity. Moreover, oligonucleotides can act as decoys particularly for transcription factors to prevent binding to the promoter. A different mode of action is the activation of Toll-like receptors to induce an immune response. Several pathways for drug development are still in their infancy, for example microRNAs and antagomirs.
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Affiliation(s)
- Fritz Eckstein
- Max-Planck-Institute for Experimental Medicine, Góttingen, Germany.
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