1
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Klabenkova KV, Zhdanova PV, Burakova EA, Bizyaev SN, Fokina AA, Stetsenko DA. A Convenient Oligonucleotide Conjugation via Tandem Staudinger Reaction and Amide Bond Formation at the Internucleotidic Phosphate Position. Int J Mol Sci 2024; 25:2007. [PMID: 38396686 PMCID: PMC10889076 DOI: 10.3390/ijms25042007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Staudinger reaction on the solid phase between an electronodeficit organic azide, such as sulfonyl azide, and the phosphite triester formed upon phosphoramidite coupling is a convenient method for the chemical modification of oligonucleotides at the internucleotidic phosphate position. In this work, 4-carboxybenzenesulfonyl azide, either with a free carboxy group or in the form of an activated ester such as pentafluorophenyl, 4-nitrophenyl, or pentafluorobenzyl, was used to introduce a carboxylic acid function to the terminal or internal internucleotidic phosphate of an oligonucleotide via the Staudinger reaction. A subsequent treatment with excess primary alkyl amine followed by the usual work-up, after prior activation with a suitable peptide coupling agent such as a uronium salt/1-hydroxybenzotriazole in the case of a free carboxyl, afforded amide-linked oligonucleotide conjugates in good yields including multiple conjugations of up to the exhaustive modification at each phosphate position for a weakly activated pentafluorobenzyl ester, whereas more strongly activated and, thus, more reactive aryl esters provided only single conjugations at the 5'-end. The conjugates synthesized include those with di- and polyamines that introduce a positively charged side chain to potentially assist the intracellular delivery of the oligonucleotide.
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Affiliation(s)
- Kristina V. Klabenkova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia;
| | - Ekaterina A. Burakova
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Sergei N. Bizyaev
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Alesya A. Fokina
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Dmitry A. Stetsenko
- Department of Physics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia; (K.V.K.); (E.A.B.); (S.N.B.); (A.A.F.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
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2
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Hill AC, Becker JP, Slominski D, Halloy F, Søndergaard C, Ravn J, Hall J. Peptide Conjugates of a 2'- O-Methoxyethyl Phosphorothioate Splice-Switching Oligonucleotide Show Increased Entrapment in Endosomes. ACS OMEGA 2023; 8:40463-40481. [PMID: 37929104 PMCID: PMC10620785 DOI: 10.1021/acsomega.3c05144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Antisense oligonucleotides (ASOs) are short, single-stranded nucleic acid molecules that alter gene expression. However, their transport into appropriate cellular compartments is a limiting factor in their potency. Here, we synthesized splice-switching oligonucleotides (SSOs) previously developed to treat the rare disease erythropoietic protoporphyria. Using chemical ligation-quantitative polymerase chain reaction (CL-qPCR), we quantified the SSOs in cells and subcellular compartments following free uptake. To drive nuclear localization, we covalently conjugated nuclear localization signal (NLS) peptides to a lead 2'-O-methoxyethyl phosphorothioate SSO using thiol-maleimide chemistry. The conjugates and parent SSO displayed similar RNA target-binding affinities. CL-qPCR quantification of the conjugates in cells and subcellular compartments following free uptake revealed one conjugate with better nuclear accumulation relative to the parent SSO. However, compared to the parent SSO, which altered the splicing of the target pre-mRNA, the conjugates were inactive at splice correction under free uptake conditions in vitro. Splice-switching activity could be conferred on the conjugates by delivering them into cells via cationic lipid-mediated transfection or by treating the cells into which the conjugates had been freely taken up with chloroquine, an endosome-disrupting agent. Our results identify the major barrier to the activity of the peptide-oligonucleotide conjugates as endosomal entrapment.
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Affiliation(s)
- Alyssa C. Hill
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - J. Philipp Becker
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - Daria Slominski
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | - François Halloy
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
| | | | - Jacob Ravn
- Roche
Innovation Center Copenhagen (RICC), Hørsholm 2970, Denmark
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich
(ETH Zürich), Zürich 8093, Switzerland
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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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Danielsen MB, Christensen NJ, Jørgensen PT, Jensen KJ, Wengel J, Lou C. Polyamine-Functionalized 2'-Amino-LNA in Oligonucleotides: Facile Synthesis of New Monomers and High-Affinity Binding towards ssDNA and dsDNA. Chemistry 2020; 27:1416-1422. [PMID: 33073896 DOI: 10.1002/chem.202004495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/16/2020] [Indexed: 12/15/2022]
Abstract
Attachment of cationic moieties to oligonucleotides (ONs) promises not only to increase the binding affinity of antisense ONs by reducing charge repulsion between the two negatively charged strands of a duplex, but also to augment their in vivo stability against nucleases. In this study, polyamine functionality was introduced into ONs by means of 2'-amino-LNA scaffolds. The resulting ONs exhibited efficient binding towards ssDNA, ssRNA and dsDNA targets, and the 2'-amino-LNA analogue carrying a triaminated linker showed the most pronounced duplex- and triplex-stabilizing effect. Molecular modelling revealed that favourable conformational and electrostatic effects led to salt-bridge formation between positively charged polyamine moieties and the Watson-Hoogsteen groove of the dsDNA targets, resulting in the observed triplex stabilization. All the investigated monomers showed increased resistance against 3'-nucleolytic digestion relative to the non-functionalized controls.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Niels Johan Christensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Knud J Jensen
- Department of Chemistry, Biomolecular Nanoscale Engineering Center, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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5
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Kye M, Zhang Z, Lim Y. Self‐assembling cyclic peptide‐oligonucleotide conjugates: Synthetic strategies and the effect of cyclic topology on self‐assembly and base pairing. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mahnseok Kye
- Department of Materials Science & Engineering Yonsei University Seoul South Korea
| | - Zhihao Zhang
- Department of Materials Science & Engineering Yonsei University Seoul South Korea
| | - Yong‐beom Lim
- Department of Materials Science & Engineering Yonsei University Seoul South Korea
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6
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Mathur D, Medintz IL. The Growing Development of DNA Nanostructures for Potential Healthcare-Related Applications. Adv Healthc Mater 2019; 8:e1801546. [PMID: 30843670 PMCID: PMC9285959 DOI: 10.1002/adhm.201801546] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/17/2019] [Indexed: 12/21/2022]
Abstract
DNA self-assembly has proven to be a highly versatile tool for engineering complex and dynamic biocompatible nanostructures from the bottom up with a wide range of potential bioapplications currently being pursued. Primary among these is healthcare, with the goal of developing diagnostic, imaging, and drug delivery devices along with combinatorial theranostic devices. The path to understanding a role for DNA nanotechnology in biomedical sciences is being approached carefully and systematically, starting from analyzing the stability and immune-stimulatory properties of DNA nanostructures in physiological conditions, to estimating their accessibility and application inside cellular and model animal systems. Much remains to be uncovered but the field continues to show promising results toward developing useful biomedical devices. This review discusses some aspects of DNA nanotechnology that makes it a favorable ingredient for creating nanoscale research and biomedical devices and looks at experiments undertaken to determine its stability in vivo. This is presented in conjugation with examples of state-of-the-art developments in biomolecular sensing, imaging, and drug delivery. Finally, some of the major challenges that warrant the attention of the scientific community are highlighted, in order to advance the field into clinically relevant applications.
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Affiliation(s)
- Divita Mathur
- Center for Bio/Molecular Science and Engineering U.S. Naval Research Laboratory Code 6910 Washington DC 20375 USA
- College of Science George Mason University Fairfax VA 22030 USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering U.S. Naval Research Laboratory Code 6907 Washington DC 20375 USA
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7
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Kye M, Lim YB. Synthesis and purification of self-assembling peptide-oligonucleotide conjugates by solid-phase peptide fragment condensation. J Pept Sci 2018; 24:e3092. [PMID: 29920844 DOI: 10.1002/psc.3092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Peptide-oligonucleotide conjugates (POCs) are interesting molecules as they covalently combine 2 of the most important biomacromolecules. Sometimes, the synthesis of POCs involves unexpected difficulties; however, POCs with self-assembling propensity are even harder to synthesize and purify. Here, we show that solid-phase peptide fragment condensation combined with thiol-maleimide or copper-catalyzed azide-alkyne cycloaddition click chemistries is useful for the syntheses of self-assembling POCs. We describe guidelines for the selection of reactive functional groups and their placement during the conjugation reaction and consider the cost-effectiveness of the reaction. Purification is another important challenge during the preparation of POCs. Our results show that polyacrylamide gel electrophoresis under denaturing conditions is most suitable to recover a high yield of self-assembling POCs. This report provides the first comprehensive study of the preparation of self-assembling POCs, which will lay a foundation for the development of elegant and sophisticated molecular assemblies.
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Affiliation(s)
- Mahnseok Kye
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, South Korea
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8
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Chen L, Fang S, Xiao X, Zheng B, Zhao M. Single-Stranded DNA Assisted Cell Penetrating Peptide-DNA Conjugation Strategy for Intracellular Imaging of Nucleases. Anal Chem 2016; 88:11306-11309. [PMID: 27934106 DOI: 10.1021/acs.analchem.6b03743] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cell penetrating peptides (CPPs) are very useful tools for delivery of DNA molecules into living cells without damaging the cell membranes. However, covalent conjugation of DNAs to CPPs is technically difficult, and the reactions between DNA and target nucleases are also liable to be affected by the cationic CPP molecules. In this work, we demonstrate that the electrostatic interactions between CPPs and single-stranded DNA (ssDNA) were stronger than those between CPP and double-stranded DNA (dsDNA). Taking advantage of this property, we developed an ssDNA protected CPP-DNA fluorescent probe which allowed for noninvasive and efficient cellular uptake and rapid imaging of target nucleases in living cells. The probe is highly sensitive and selective. This work represents the first example of using CPP-DNA conjugate to deliver DNA fluorescent probes for in situ imaging of nucleases within cells. The developed approach also holds great potential for the cellular delivery of other nucleic acid molecules for diagnosis or therapeutics purposes.
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Affiliation(s)
- Lu Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Simin Fang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, Hubei 430030, China
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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9
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Hayashi J, Hamada T, Sasaki I, Nakagawa O, Wada SI, Urata H. Synthesis of novel cationic spermine-conjugated phosphotriester oligonucleotide for improvement of cell membrane permeability. Bioorg Med Chem Lett 2015; 25:3610-5. [PMID: 26149182 DOI: 10.1016/j.bmcl.2015.06.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 11/17/2022]
Abstract
A spermine-conjugated ethyl phosphotriester oligonucleotide was obtained by solid-phase synthesis based on phosphoramidite chemistry. The ethyl phosphotriester linkage was robust to exonuclease digestion and stable in fetal bovine serum. Cell membrane permeability of the spermine-conjugated ethyl phosphotriester oligonucleotide was studied by fluorescence experiments. The effective cell penetrating potency of the spermine-conjugated ethyl phosphotriester oligonucleotide was determined by confocal laser scanning microscopy and measurement of intracellular fluorescence intensity.
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Affiliation(s)
- Junsuke Hayashi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Tomoko Hamada
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Ikumi Sasaki
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Osamu Nakagawa
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shun-ichi Wada
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Hidehito Urata
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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10
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James C, Rush AM, Insley T, Vuković L, Adamiak L, Král P, Gianneschi NC. Poly(oligonucleotide). J Am Chem Soc 2014; 136:11216-9. [PMID: 25077676 PMCID: PMC4140503 DOI: 10.1021/ja503142s] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Indexed: 01/01/2023]
Abstract
Here we report the preparation of poly(oligonucleotide) brush polymers and amphiphilic brush copolymers from nucleic acid monomers via graft-through polymerization. We describe the polymerization of PNA-norbornyl monomers to yield poly-PNA (poly(peptide nucleic acid)) via ring-opening metathesis polymerization (ROMP) with the initiator, (IMesH2)(C5H5N)2(Cl)2RuCHPh.1 In addition, we present the preparation of poly-PNA nanoparticles from amphiphilic block copolymers and describe their hybridization to a complementary single-stranded DNA (ssDNA) oligonucleotide.
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Affiliation(s)
- Carrie
R. James
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Anthony M. Rush
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Thomas Insley
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lela Vuković
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lisa Adamiak
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Petr Král
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Nathan C. Gianneschi
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
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11
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Lee MK, Lim YB. Facile synthesis, optical and conformational characteristics, and efficient intracellular delivery of a peptide-DNA conjugate. Bioorg Med Chem 2014; 22:4204-9. [PMID: 24924424 DOI: 10.1016/j.bmc.2014.05.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/17/2014] [Accepted: 05/19/2014] [Indexed: 12/01/2022]
Abstract
Covalent conjugation of disparate peptide and oligonucleotide biomacromolecular species produces peptide-oligonucleotide conjugates (POCs), which are interesting molecules with great potential for use in diverse bioapplications. However, peptide-oligonucleotide conjugation methods are not well established, and the intracellular delivery efficacy of POCs is debatable. Here, we describe a simple method for the synthesis and purification of POCs. When peptides are carefully designed to have a near-neutral charge state, a relatively hydrophobic polarity, and receptor-targeting ligands, synthesis and purification become highly efficient and straightforward. UV-vis, fluorescence, and circular dichroism studies show that both types of molecules mutually influence each other, changing their optical and conformational characteristics in the context of POCs. The combined effect of peptide design strategy, targeting ligands, and relatively hydrophobic property, enables the efficient cellular delivery of POCs.
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Affiliation(s)
- Mun-kyung Lee
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Republic of Korea
| | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Republic of Korea.
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12
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Oligonucleotide-peptide conjugates: solid-phase synthesis under acidic conditions and use in ELISA assays. Molecules 2012; 17:13825-43. [PMID: 23174899 PMCID: PMC6268656 DOI: 10.3390/molecules171213825] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/16/2012] [Accepted: 11/16/2012] [Indexed: 11/17/2022] Open
Abstract
Here we used solid-phase methods to prepare oligonucleotides carrying fibrin/ filaggrin citrullinated peptides. Post-synthetic conjugation protocols were successfully applied for the synthesis of oligonucleotides carrying small peptides. A stepwise protocol using acid treatment for the final deprotection allowed the preparation of polypyrimidine oligonucleotides carrying longer and arginine-rich peptides. An ELISA-based test using the oligonucleotide-citrullinated peptide conjugates was developed for the detection of anti-citrullinated protein/peptide antibodies in human serum from rheumatoid arthritis patients.
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13
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Zhou G, Khan F, Dai Q, Sylvester JE, Kron SJ. Photocleavable peptide-oligonucleotide conjugates for protein kinase assays by MALDI-TOF MS. MOLECULAR BIOSYSTEMS 2012; 8:2395-404. [PMID: 22772337 DOI: 10.1039/c2mb25163a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Robust methods for highly parallel, quantitative analysis of cellular protein tyrosine kinase activities may provide tools critically needed to decipher oncogenic signaling, discover new targeted drugs, diagnose cancer and monitor patients. Here, we describe proof-of-principle for a novel protein kinase assay with the potential to help overcome these challenges. MALDI-TOF mass spectrometry provides an ideal tool for label-free multiplexed analysis of peptide phosphorylation, but is poorly matched to homogeneous assays and complex samples. Thus, we conjugated a common oligonucleotide tag to multiple peptide substrates, offering efficient capture from solution-phase kinase reactions by annealing to the complementary sequence tethered to PEG-passivated superparamagnetic microparticles. To enable reversible conjugation, we developed a novel bifunctional cross-linker allowing simple and efficient preparation of photocleavable peptide-oligonucleotide conjugates. After washing away contaminants and following photorelease, MALDI-TOF analysis yielded relative phosphorylation of each peptide with high sensitivity and specificity. Validating the hybridization-mediated multiplexed kinase assay, when three peptide substrate-oligonucleotide conjugates were mixed with the tyrosine kinase c-Abl and ATP, we readily observed their differential phosphorylation yet measured a common IC(50) for the Abl kinase inhibitor imatinib. This new assay enables analysis of protein kinase activities in a multiplexed format amenable to screening inhibitors against multiple kinases in parallel, an important capability for drug discovery and predictive diagnostics.
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Affiliation(s)
- Guangchang Zhou
- Department of Molecular Genetics and Cell Biology, Gordon Center for Integrative Sciences, W522A, The University of Chicago, Chicago, IL 60637, USA
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14
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Rahman SMA, Baba T, Kodama T, Islam MA, Obika S. Hybridizing ability and nuclease resistance profile of backbone modified cationic phosphorothioate oligonucleotides. Bioorg Med Chem 2012; 20:4098-102. [PMID: 22658536 DOI: 10.1016/j.bmc.2012.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/01/2012] [Accepted: 05/02/2012] [Indexed: 11/25/2022]
Abstract
Various stereochemically pure cationic phosphorothioate oligonucleotides bearing aminoalkyl moieties were synthesized, and their duplex-forming ability against single-stranded DNA (ssDNA), single-stranded RNA (ssRNA) and triplex-forming ability against double-stranded DNA (dsDNA) were evaluated by UV melting experiments. The cationic Rp stereoisomers showed improved duplex-forming ability against ssDNA, triplex-forming ability against dsDNA and nuclease stability.
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Affiliation(s)
- S M Abdur Rahman
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
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15
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Pyridylthiourea-grafted polyethylenimine offers an effective assistance to siRNA-mediated gene silencing in vitro and in vivo. J Control Release 2012; 157:418-26. [DOI: 10.1016/j.jconrel.2011.10.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 10/05/2011] [Accepted: 10/06/2011] [Indexed: 12/15/2022]
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16
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Wenska M, Alvira M, Steunenberg P, Stenberg Å, Murtola M, Strömberg R. An activated triple bond linker enables 'click' attachment of peptides to oligonucleotides on solid support. Nucleic Acids Res 2011; 39:9047-59. [PMID: 21795380 PMCID: PMC3203603 DOI: 10.1093/nar/gkr603] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 07/05/2011] [Accepted: 07/06/2011] [Indexed: 11/13/2022] Open
Abstract
A general procedure, based on a new activated alkyne linker, for the preparation of peptide-oligonucleotide conjugates (POCs) on solid support has been developed. With this linker, conjugation is effective at room temperature (RT) in millimolar concentration and submicromolar amounts. This is made possible since the use of a readily attachable activated triple bond linker enhances the Cu(I) catalyzed 1,3-dipolar cycloaddition ('click' reaction). The preferred scheme for conjugate preparation involves sequential conjugation to oligonucleotides on solid support of (i) an H-phosphonate-based aminolinker; (ii) the triple bond donor p-(N-propynoylamino)toluic acid (PATA); and (iii) azido-functionalized peptides. The method gives conversion of oligonucleotide to the POC on solid support, and only involves a single purification step after complete assembly. The synthesis is flexible and can be carried out without the need for specific automated synthesizers since it has been designed to utilize commercially available oligonucleotide and peptide derivatives on solid support or in solution. Methodology for the ready conversion of peptides into 'clickable' azidopeptides with the possibility of selecting either N-terminus or C-terminus connection also adds to the flexibility and usability of the method. Examples of synthesis of POCs include conjugates of oligonucleotides with peptides known to be membrane penetrating and nuclear localization signals.
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Affiliation(s)
- Malgorzata Wenska
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, SE-141 83 Huddinge, Sweden
| | | | | | | | | | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, SE-141 83 Huddinge, Sweden
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17
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Sánchez A, Pedroso E, Grandas A. Maleimide-dimethylfuran exo adducts: effective maleimide protection in the synthesis of oligonucleotide conjugates. Org Lett 2011; 13:4364-7. [PMID: 21790151 DOI: 10.1021/ol201690b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The reaction of maleimide-containing compounds with 2,5-dimethylfuran gives a mixture of exo and endo isomers from which the exo cycloadduct can be easily isolated taking advantage of its stability in concentrated aqueous ammonia. Bifunctional compounds incorporating a dimethylfuran-protected maleimide (exo adduct) have been attached to resin-linked oligonucleotide chains. Removal of protecting groups masking oligonucleotide functionalities followed by retro-Diels-Alder maleimide deprotection affords maleimido-oligonucleotides suitable for conjugation, as assessed by their reaction with different thiols.
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Affiliation(s)
- Albert Sánchez
- Departament de Química Orgànica and IBUB, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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18
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Gagnon KT, Watts JK, Pendergraff HM, Montaillier C, Thai D, Potier P, Corey DR. Antisense and antigene inhibition of gene expression by cell-permeable oligonucleotide-oligospermine conjugates. J Am Chem Soc 2011; 133:8404-7. [PMID: 21539318 PMCID: PMC3106116 DOI: 10.1021/ja200312y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oligonucleotides and their derivatives are a proven chemical strategy for modulating gene expression. However, their negative charge remains a challenge for delivery and target recognition inside cells. Here we show that oligonucleotide-oligospermine conjugates (Zip nucleic acids or ZNAs) can help overcome these shortcomings by serving as effective antisense and antigene agents. Conjugates containing DNA and locked nucleic acid (LNA) oligonucleotides are active, and oligospermine conjugation facilitates carrier-free cell uptake at nanomolar concentrations. Conjugates targeting the CAG triplet repeat within huntingtin (HTT) mRNA selectively inhibit expression of the mutant huntingtin protein. Conjugates targeting the promoter of the progesterone receptor (PR) function as antigene agents to block PR expression. These observations support further investigation of ZNA conjugates as gene silencing agents.
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Affiliation(s)
- Keith T. Gagnon
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Jonathan K. Watts
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | - Hannah M. Pendergraff
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
| | | | - Danielle Thai
- SIGMA Custom Products, Genopole Campus 1, 5 rue Desbruères, 91030 Evry Cedex, France
| | - Pierre Potier
- SIGMA Custom Products, Genopole Campus 1, 5 rue Desbruères, 91030 Evry Cedex, France
| | - David R. Corey
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390, USA
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19
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Foillard S, Zuber G, Doris E. Polyethylenimine-carbon nanotube nanohybrids for siRNA-mediated gene silencing at cellular level. NANOSCALE 2011; 3:1461-1464. [PMID: 21301705 DOI: 10.1039/c0nr01005g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Carbon nanotubes (CNTs) covalently modified with low molecular weight polyethylenimine (PEI) are able to bind and deliver siRNA to cells with higher efficacy than a reference lipidic carrier. The performances of the nanohybrid are rationalized by the combination of the cell penetration and endosomal escape properties of CNTs and PEI, respectively.
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Affiliation(s)
- Stéphanie Foillard
- CEA, iBiTecS, Service de Chimie Bioorganique et de Marquage, 91191, Gif-sur-Yvette, France
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20
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Murtola M, Zaramella S, Yeheskiely E, Strömberg R. Cationic peptides that increase the thermal stabilities of 2'-O-MeRNA/RNA duplexes but do not affect DNA/DNA melting. Chembiochem 2011; 11:2606-12. [PMID: 21110373 DOI: 10.1002/cbic.201000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Several different cationic nonapeptides have been synthesized and investigated with respect to how they can influence the thermal melting of 2'-O-methylRNA/RNA and DNA/DNA duplexes. Each peptide has a C-terminal L-phenylalanine unit and is otherwise uniformly composed of a sequence of a specific basic D-amino acid that in most cases will be largely charged at neutral pH. These N-terminal octamer stretches are composed variously of the amino acids D-lysine, D-diaminobutyric acid (D-Dab), D-diaminopropionic acid (D-Dap), or D-histidine. None of the peptides substantially affected the thermal melting of DNA/DNA duplexes, which was in sharp contrast with their effects on 2'-O-methylRNA/RNA duplexes. In particular, the peptides based on diaminopropionic and diaminobutyric acid units had strong positive effects on the melting temperatures of the 2'-O-methylRNA duplexes (up to 16 °C higher with 1 equivalent of peptide) at pH 7, whereas at pH 6 the effect was even more drastic (ΔT(m) up to +25 °C). The shorter R groups of the Dap and Dab groups appear to have a better length than lysine for enhancement of the thermal melting of the 2'-O-methylRNA/RNA duplex, an effect that is more pronounced at lower pH but substantial even at pH 7, although the Dap derivative is not likely to be fully protonated. The dramatic difference between the influence, or lack thereof, on the 2'-O-methylRNA/RNA and the DNA/DNA thermal meltings suggest that, although electrostatic interactions probably play a role, there is another major and structurally dependent component influencing the properties of the duplexes. This is also seen in the observation that the oligo-Dap and oligo-Dab peptides give greater melting point enhancements than both the lysine peptide (with a longer side chain) and a β-linked Dap peptide with a shorter side chain and a longer backbone.
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Affiliation(s)
- Merita Murtola
- Department of Biosciences and Nutrition, Unit for Bioorganic Chemistry, Karolinska Institutet, 14183 Huddinge, Sweden
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21
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Wang TP, Chiou YJ, Chen Y, Wang EC, Hwang LC, Chen BH, Chen YH, Ko CH. Versatile phosphoramidation reactions for nucleic acid conjugations with peptides, proteins, chromophores, and biotin derivatives. Bioconjug Chem 2010; 21:1642-55. [PMID: 20690641 DOI: 10.1021/bc1001505] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chemical conjugations of nucleic acids with macromolecules or small molecules are common approaches to study nucleic acids in chemistry and biology and to exploit nucleic acids for medical applications. The conjugation of nucleic acids such as oligonucleotides with peptides is especially useful to circumvent cell delivery and specificity problems of oligonucleotides as therapeutic agents. However, current approaches are limited and inefficient in their ability to afford peptide-oligonucleotide conjugates (POCs). Here, we report an effective and reproducible approach to prepare POCs and other nucleic acid conjugates based on a newly developed nucleic acid phosphoramidation method. The development of a new nucleic acid phosphoramidation reaction was achieved by our successful synthesis of a novel amine-containing biotin derivative used to systematically optimize the reactions. The improved phosphoramidation reactions dramatically increased yields of nucleic acid-biotin conjugates up to 80% after 3 h reaction. Any nucleic acids with a terminal phosphate group are suitable reactants in phosphoramidation reactions to conjugate with amine-containing molecules such as biotin and fluorescein derivatives, proteins, and, most importantly, peptides to enable the synthesis of POCs for therapeutic applications. Polymerase chain reactions (PCRs) to study incorporation of biotin or fluorescein-tagged DNA primers into the reaction products demonstrated that appropriate controls of nucleic acid phosphoramidation reactions incur minimum adverse effects on inherited base-pairing characteristics of nucleotides in nucleic acids. The phosphoramidation approach preserves the integrity of hybridization specificity in nucleic acids when preparing POCs. By retaining integrity of the nucleic acids, their effectiveness as therapeutic reagents for gene silencing, gene therapy, and RNA interference is ensured. The potential for POC use was demonstrated by two-step phosphoramidation reactions to successfully synthesize nucleic acid-tetraglycine conjugates. In addition, phosphoramidation reactions provided a facile approach to prepare nucleic acid-BSA conjugates with good yields. In summary, the new approach to phosphoramidation reactions offers a universal method to prepare POCs and other nucleic acid conjugates with high yields in aqueous solutions. The methods can be easily adapted to typical chemistry or biology laboratory setups which will expedite the applications of POCs for basic research and medicine.
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Affiliation(s)
- Tzu-Pin Wang
- Department of Medicinal and Applied Chemistry, Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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22
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Marlin F, Simon P, Saison-Behmoaras T, Giovannangeli C. Delivery of oligonucleotides and analogues: the oligonucleotide conjugate-based approach. Chembiochem 2010; 11:1493-500. [PMID: 20575132 DOI: 10.1002/cbic.201000138] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Fanny Marlin
- Museum National d'Histoire Naturelle, CNRS, UMR7196, Inserm, U565, 43 rue Cuvier, 75005 Paris, France
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23
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Fuchs S, Winter G, Coester C. Ultrasonic resonator technology as a new quality control method evaluating gelatin nanoparticles. J Microencapsul 2010; 27:242-52. [PMID: 20406094 DOI: 10.3109/02652040903079534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Nanomedicine is a quickly evolving field where more and more possible applications become evident and start entering clinical trials or even the market. However, the analytic methods are not always able to keep pace with the new formulations' demands. One example of a promising medical implementation is oligodeoxynucleotide (ODN) delivery by gelatin nanoparticles (GNPs). Currently, quality control is dependent on either some time consuming or destructive spectrometric, chromatographic or electrophoretic methods. A possible enlargement of the portfolio by Ultrasonic Resonator Technology (URT) is investigated here by subjecting plain GNPs in various sizes and concentrations as well as ODN-loaded GNPs to URT analysis. If calibrated by photon correlation spectroscopy (PCS) and other spectroscopy methods for each single nanoparticle system parameter, URT is an efficient and non-destructive technique and serves as a broad characterization method. URT is emphasized to play a possible future part in the size, concentration and ODN loading monitoring, e.g. of gelatin nanoparticles in the course of formulation development.
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Affiliation(s)
- Sebastian Fuchs
- Department of Pharmacy, Pharmaceutical Technology and Biopharmacy, Ludwig Maximilians University, Munich, Germany
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24
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Alatorre-Meda M, Taboada P, Krajewska B, Willemeit M, Deml A, Klösel R, Rodríguez JR. DNA−Poly(diallyldimethylammonium chloride) Complexation and Transfection Efficiency. J Phys Chem B 2010; 114:9356-66. [DOI: 10.1021/jp1016856] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Manuel Alatorre-Meda
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Pablo Taboada
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Barbara Krajewska
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Markus Willemeit
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Alexander Deml
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Roland Klösel
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
| | - Julio R. Rodríguez
- Grupo de Nanomateriales y Materia Blanda, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Grupo de Física de Coloides y Polímeros, Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Faculty of Chemistry, Jagiellonian University, 30-060 Kraków, Ingardena 3, Poland; and Biontex Laboratories GmbH, D-82152
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25
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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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26
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Klein E, Ciobanu M, Klein J, Machi V, Leborgne C, Vandamme T, Frisch B, Pons F, Kichler A, Zuber G, Lebeau L. "HFP" fluorinated cationic lipids for enhanced lipoplex stability and gene delivery. Bioconjug Chem 2010; 21:360-71. [PMID: 20099841 DOI: 10.1021/bc900469z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although a great number of cationic lipids have been designed and evaluated as gene delivery systems, there is still a need for improvement of nonviral vectors. Recently, cationic lipids incorporating terminal fluoroalkyl segments ("FHP" lipids) have been described to display remarkable transfection potency. Here, we describe the synthesis of a new family of fluorinated triblock cationic lipids in which a fluorous segment lays between the cationic and the lipophilic parts of the molecule ("HFP" lipids). The compounds were designed so their self-assembly would offer enhanced resistance toward the host's degradation mechanisms mediated by lipophilic insertion. Self-assembly properties of these cationic lipids were evaluated at the air-water interface where they collapse in a highly ordered liquid phase. The HFP lipids efficiently condense DNA, and the resulting lipoplexes display enhanced resistance to amphiphilic agents when compared to nonfluorinated or FHP cationic lipids. Transfection properties of the fluorinated vectors, alone or as mixtures with different helper lipids (DOPE and a fluorinated analogue of DOPE), were then investigated on different cell lines (BHK-21, HepG2, and HeLa) and compared to those of the reference cationic lipid DOTAP. Data show that impermeabilization of the lipidic phase by fluorous segments alter significantly the gene transfection activities. Remarkably, incorporation of DOPE within the lipoplexes provides the particles with high gene transfection activity without reducing their resistance to amphiphilic agents.
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Affiliation(s)
- Emmanuel Klein
- Laboratoire de Conception et Application de Molecules Bioactives, CNRS-Universite de Strasbourg, 74 route du Rhin, BP 60024, 67401 Illkirch Cedex, France
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27
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Creusat G, Rinaldi AS, Weiss E, Elbaghdadi R, Remy JS, Mulherkar R, Zuber G. Proton Sponge Trick for pH-Sensitive Disassembly of Polyethylenimine-Based siRNA Delivery Systems. Bioconjug Chem 2010; 21:994-1002. [DOI: 10.1021/bc100010k] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gaelle Creusat
- Laboratoire de Conception et Application de Molécules Bioactives, CNRS-Université de Strasbourg UMR 7199, Faculté de Pharmacie, 74, route du Rhin, 67400 Illkirch, France, ESBS - FRE 3211, Immunobiotechnologie Bld., Sébastien Brant BP, 10413 F-67412 Illkirch, France, and ACTREC, Tata Memorial Centre Kharghar, Navi Mumbai 410210, India
| | - Anne-Sophie Rinaldi
- Laboratoire de Conception et Application de Molécules Bioactives, CNRS-Université de Strasbourg UMR 7199, Faculté de Pharmacie, 74, route du Rhin, 67400 Illkirch, France, ESBS - FRE 3211, Immunobiotechnologie Bld., Sébastien Brant BP, 10413 F-67412 Illkirch, France, and ACTREC, Tata Memorial Centre Kharghar, Navi Mumbai 410210, India
| | - Etienne Weiss
- Laboratoire de Conception et Application de Molécules Bioactives, CNRS-Université de Strasbourg UMR 7199, Faculté de Pharmacie, 74, route du Rhin, 67400 Illkirch, France, ESBS - FRE 3211, Immunobiotechnologie Bld., Sébastien Brant BP, 10413 F-67412 Illkirch, France, and ACTREC, Tata Memorial Centre Kharghar, Navi Mumbai 410210, India
| | - Rkia Elbaghdadi
- Laboratoire de Conception et Application de Molécules Bioactives, CNRS-Université de Strasbourg UMR 7199, Faculté de Pharmacie, 74, route du Rhin, 67400 Illkirch, France, ESBS - FRE 3211, Immunobiotechnologie Bld., Sébastien Brant BP, 10413 F-67412 Illkirch, France, and ACTREC, Tata Memorial Centre Kharghar, Navi Mumbai 410210, India
| | - Jean-Serge Remy
- Laboratoire de Conception et Application de Molécules Bioactives, CNRS-Université de Strasbourg UMR 7199, Faculté de Pharmacie, 74, route du Rhin, 67400 Illkirch, France, ESBS - FRE 3211, Immunobiotechnologie Bld., Sébastien Brant BP, 10413 F-67412 Illkirch, France, and ACTREC, Tata Memorial Centre Kharghar, Navi Mumbai 410210, India
| | - Rita Mulherkar
- Laboratoire de Conception et Application de Molécules Bioactives, CNRS-Université de Strasbourg UMR 7199, Faculté de Pharmacie, 74, route du Rhin, 67400 Illkirch, France, ESBS - FRE 3211, Immunobiotechnologie Bld., Sébastien Brant BP, 10413 F-67412 Illkirch, France, and ACTREC, Tata Memorial Centre Kharghar, Navi Mumbai 410210, India
| | - Guy Zuber
- Laboratoire de Conception et Application de Molécules Bioactives, CNRS-Université de Strasbourg UMR 7199, Faculté de Pharmacie, 74, route du Rhin, 67400 Illkirch, France, ESBS - FRE 3211, Immunobiotechnologie Bld., Sébastien Brant BP, 10413 F-67412 Illkirch, France, and ACTREC, Tata Memorial Centre Kharghar, Navi Mumbai 410210, India
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28
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Singh Y, Murat P, Defrancq E. Recent developments in oligonucleotide conjugation. Chem Soc Rev 2010; 39:2054-70. [PMID: 20393645 DOI: 10.1039/b911431a] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Synthetic oligonucleotides (ONs) are being investigated for various therapeutic and diagnostic applications. The interest in ONs arises because of their capability to cause selective inhibition of gene expression by binding to the target DNA/RNA sequences through mechanisms such as antigene, antisense, and RNA interference. ONs with catalytic activity (ribozymes and DNAzymes) against the target sequences, and ability to bind to the target molecules (aptamers), ranging from small molecules to proteins, are also known. Therefore ONs are considered potentially useful for the treatment of viral diseases and cancer. ONs also find use in the design of DNA microchips (a powerful bio-analytical tool) and novel materials in nanotechnology. However, the clinical success achieved so far with ONs has not been satisfactory, and the major impediments have been recognised as their instability against nucleases, lack of target specificity, and poor uptake and targeted delivery. Tremendous efforts have been made to improve the ON properties by either incorporating chemical modifications in the ON structure or covalently linking (conjugation) reporter groups, with biologically relevant properties, to ONs. Conjugation is of great interest because it can be used not only to improve the existing ON properties but also to impart entirely new properties. This tutorial review focuses on the recent developments in ON conjugation, and describes the key challenges in efficient ON conjugation and major synthetic approaches available for successful ON conjugate syntheses. In addition, an overview on major classes of ON conjugates along with their use in therapeutics, diagnostics and nanotechnology is provided.
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Affiliation(s)
- Yashveer Singh
- Départment of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
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29
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Godeau G, Arnion H, Brun C, Staedel C, Barthélémy P. Fluorocarbon oligonucleotide conjugates for nucleic acids delivery. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00054j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Alatorre-Meda M, González-Pérez A, Rodríguez JR. DNA–METAFECTENE™ PRO complexation: a physical chemistry study. Phys Chem Chem Phys 2010; 12:7464-72. [DOI: 10.1039/b920900j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Santhiya D, Dias RS, Shome A, Das PK, Miguel MG, Lindman B, Maiti S. Role of linker groups between hydrophilic and hydrophobic moieties of cationic surfactants on oligonucleotide-surfactant interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:13770-13775. [PMID: 19681626 DOI: 10.1021/la901546t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The interaction between DNA and amino-acid-based surfactants with different linker groups was investigated by gel electrophoresis, ethidium bromide exclusion assays, circular dichroism, and melting temperature determinations. The studies showed that the strength of the interaction between the oligonucleotides and the surfactants is highly dependent on the linker of the surfactant. For ester surfactants, no significant interaction was observed for surfactant-to-DNA charge ratios up to 12. On the other hand, amide surfactants were shown to interact strongly with the oligonucleotides; these surfactants could displace up to 75% of the ethidium bromide molecules bound to the DNA and induced significant changes in the circular dichroism spectra. When comparing the headgroups of the surfactants, it was observed that surfactants with more hydrophobic headgroups (proline vs alanine) interacted more strongly with the DNA, in good agreement with previous studies.
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Affiliation(s)
- Deenan Santhiya
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Liu L, Zhang H, Meng X, Yin J, Li D, Liu C. Dinuclear metal(II) complexes of polybenzimidazole ligands as carriers for DNA delivery. Biomaterials 2009; 31:1380-91. [PMID: 19906419 DOI: 10.1016/j.biomaterials.2009.10.056] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 10/25/2009] [Indexed: 11/27/2022]
Abstract
A metal-based nonviral carrier for DNA-transfer in gene therapy was synthesized and characterized. The strong intermolecular pi-pi contacts are common in the observed dinuclear Cu(2+) and Co(2+) complexes of polybenzimidazole ligands. The affinity assays indicated that the strong binding of the complexes to DNA is driven by both electrostatic attractions between the complexes and DNA and the intercalation of the ligands between DNA base pairs. The typical in vitro studies showed that micromolar doses of each complex tested can efficiently and rapidly condense free DNA, either in linear or circular state, from solutions into well defined and globular nanoparticles with varied sizes. Therefore, the formation and dissociation of the DNA condensates were explored in detail under different conditions, indicating that the sizes of DNA condensates can be regulated by changing both doses and incubation time for the different dinuclear complexes. Since the intermolecular pi-pi interactions in the DNA-bound complexes may be a key force to drive DNA condensation, we propose a new DNA condensation model that is essentially distinct from that proposed for the most studied multivalent cationic reagents used in DNA condensation. The cellular uptake experiments successfully performed with the DNA condensates including plasmid pGL3 control vector that strongly expresses luciferase in many types of mammalian cells, as well as cytotoxicity evaluation, demonstrated the potentiality of the dinuclear metal(II) complexes as a new nonviral gene carrier. Finally, the dinuclear Co(2+) complexes of polybenzimidazole ligands are suggested to be the most potential nonviral gene carriers that are not impacted by serum proteins.
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Affiliation(s)
- Liang Liu
- Department of Chemistry, Huazhong University of Science and Technology, Wuhan 430074, China
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Creusat G, Zuber G. Self-Assembling Polyethylenimine Derivatives Mediate Efficient siRNA Delivery in Mammalian Cells. Chembiochem 2008; 9:2787-9. [DOI: 10.1002/cbic.200800540] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Godeau G, Staedel C, Barthélémy P. Lipid-conjugated oligonucleotides via "click chemistry" efficiently inhibit hepatitis C virus translation. J Med Chem 2008; 51:4374-6. [PMID: 18605715 DOI: 10.1021/jm800518u] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Conjugation of a lipid moiety via "click chemistry" potentiates the cellular uptake of oligonucleotides and allows their intracellular delivery. These nontoxic lipid conjugates efficiently inhibit hepatitis C virus internal ribosome entry site (IRES)-mediated translation in human hepatic Huh7 cells. The biological activity of the lipid-conjugated oligonucleotides is not affected by the presence of serum.
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Jadhav V, Maiti S, Dasgupta A, Das PK, Dias RS, Miguel MG, Lindman B. Effect of the Head-Group Geometry of Amino Acid-Based Cationic Surfactants on Interaction with Plasmid DNA. Biomacromolecules 2008; 9:1852-9. [DOI: 10.1021/bm8000765] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Winkler J, Noe CR. Oligonucleotide charge reversal: 2'-O-lysylaminohexyl modified oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:939-42. [PMID: 18058513 DOI: 10.1080/15257770701507978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A novel cationic building nucleoside building block designed for antisense and siRNA oligonucleotides is presented. Protected L-lysine was coupled to 2'-O-aminohexyluridine and the resulting nucleoside was phosphitylated for automated oligonucleotide synthesis. An increasing number of these 2'-O-lysylaminohexyl nucleosides lowered the melting temperature of desoxy-thymidine homododecamers, but the decrease was lower than that for DNA/RNA hybrids. Incubation with an exonuclease showed the exceptionally high resistance against enzymatic degradation. CD spectrometry revealed a gradual transition towards an A-type oligonucleotide structure. Based on these data, the cationic building block is particularly suited for gapmer antisense as well as siRNA oligonucleotides.
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Affiliation(s)
- Johannes Winkler
- Department of Medicinal Chemistry, University of Vienna, Vienna, Austria.
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Giljohann DA, Seferos DS, Patel PC, Millstone JE, Rosi NL, Mirkin CA. Oligonucleotide loading determines cellular uptake of DNA-modified gold nanoparticles. NANO LETTERS 2007; 7:3818-21. [PMID: 17997588 PMCID: PMC8585332 DOI: 10.1021/nl072471q] [Citation(s) in RCA: 411] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The cellular internalization of oligonucleotide-modified nanoparticles is investigated. Uptake is dependent on the density of the oligonucleotide loading on the surface of the particles, where higher densities lead to greater uptake. Densely functionalized nanoparticles adsorb a large number of proteins on the nanoparticle surface. Nanoparticle uptake is greatest where a large number of proteins are associated with the particle.
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Affiliation(s)
| | | | | | | | | | - Chad A. Mirkin
- To whom correspondence should be addressed. Fax: (+1) 847-467-5123.
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Gogoi K, Mane MV, Kunte SS, Kumar VA. A versatile method for the preparation of conjugates of peptides with DNA/PNA/analog by employing chemo-selective click reaction in water. Nucleic Acids Res 2007; 35:e139. [PMID: 17981837 PMCID: PMC2175367 DOI: 10.1093/nar/gkm935] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The specific 1,3 dipolar Hüisgen cycloaddition reaction known as 'click-reaction' between azide and alkyne groups is employed for the synthesis of peptide-oligonucleotide conjugates. The peptide nucleic acids (PNA)/DNA and peptides may be appended either by azide or alkyne groups. The cycloaddition reaction between the azide and alkyne appended substrates allows the synthesis of the desired conjugates in high purity and yields irrespective of the sequence and functional groups on either of the two substrates. The versatile approach could also be employed to generate the conjugates of peptides with thioacetamido nucleic acid (TANA) analog. The click reaction is catalyzed by Cu (I) in either water or in organic medium. In water, approximately 3-fold excess of the peptide-alkyne/azide drives the reaction to completion in 2 h with no side products.
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Affiliation(s)
- Khirud Gogoi
- Division of Organic Chemistry, National Chemical Laboratory, Pune, India
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Voirin E, Behr JP, Kotera M. Versatile synthesis of oligodeoxyribonucleotide-oligospermine conjugates. Nat Protoc 2007; 2:1360-7. [PMID: 17545974 DOI: 10.1038/nprot.2007.177] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A protocol for the rapid, automated synthesis of oligospermine-oligonucleotide sequences is described. To this end, a protected spermine phosphoramidite derivative was synthesized in six steps from spermine and used as the fifth synthon in an oligonucleotide synthesizer. Parameters were optimized to reach greater than 95% coupling yields. Cationic oligonucleotides show enhanced hybridization and strand invasion properties, and hence are an alternative to conventional oligonucleotides for molecular biology, diagnostic and potential therapeutic applications. A multi-gram-scale synthesis of the spermine phosphoramidite allowing several hundred coupling steps takes 2-3 weeks. Oligonucleotide synthesis and purification takes approximately 3 d.
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Affiliation(s)
- Emilie Voirin
- Polyplus-transfection SA, Bioparc, Boulevard S. Brandt, BP90018, 67401 Illkirch, France
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