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Gras M, Adler P, Smietana M. A Catalytic Approach for the Synthesis of Peptide-Oligonucleotides Conjugates in Aqueous Solution or On-Column. Chemistry 2024; 30:e202401069. [PMID: 38709711 DOI: 10.1002/chem.202401069] [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: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
Peptide-oligonucleotide conjugates (POCs) are covalent architectures composed of a DNA or RNA molecules linked to a peptide. These constructs have found widespread applications ranging from hybrid nanomaterials to gene-targeted therapies. Considering the important role of POCs, a new catalytic approach for their preparation is reported here, that could be applied either on solid support in anhydrous media, or post-synthetically in aqueous buffer. Single amino acids, peptides and cell penetrating peptides (CPPs) were conjugated to various oligo(ribo)nucleotides with high conversions and good isolated yields. The applicability of the method was demonstrated on more than 35 examples including an analogue of a commercial therapeutic oligonucleotide. Other conjugation partners, such as deoxycholic acid and biotin were also successfully conjugated to oligonucleotides. To highlight the potential of this catalytic approach, these conditions have been applied to iterative processes, which is of high interest for the development of DNA-Encoded Libraries.
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Affiliation(s)
- Marion Gras
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Pauline Adler
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Michael Smietana
- IBMM, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34293, Montpellier Cedex 5, France
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2
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Klabenkova K, Fokina A, Stetsenko D. Chemistry of Peptide-Oligonucleotide Conjugates: A Review. Molecules 2021; 26:5420. [PMID: 34500849 PMCID: PMC8434111 DOI: 10.3390/molecules26175420] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/25/2022] Open
Abstract
Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.
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Affiliation(s)
- Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alesya Fokina
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
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3
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Devaux A, Bonnat L, Lavergne T, Defrancq E. Access to a stabilized i-motif DNA structure through four successive ligation reactions on a cyclopeptide scaffold. Org Biomol Chem 2020; 18:6394-6406. [DOI: 10.1039/d0ob01311k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Four successive chemical ligations were used for the assembly of a sophisticated biomolecular system allowing the formation of a stabilized i-motif DNA at pH 7.
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Affiliation(s)
- Alexandre Devaux
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
| | - Laureen Bonnat
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
| | - Thomas Lavergne
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
| | - Eric Defrancq
- Univ. Grenoble Alpes
- Département de Chimie Moléculaire
- CNRS
- Grenoble 38000
- France
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4
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Probst N, Lartia R, Théry O, Alami M, Defrancq E, Messaoudi S. Efficient Buchwald-Hartwig-Migita Cross-Coupling for DNA Thioglycoconjugation. Chemistry 2018; 24:1795-1800. [PMID: 29205564 DOI: 10.1002/chem.201705371] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 11/11/2022]
Abstract
An efficient method for the thioglycoconjugation of iodinated oligonucleotides by Buchwald-Hartwig-Migita cross-coupling under mild conditions is reported. The method enables divergent synthesis of many different functionalized thioglycosylated ODNs in good yields, without affecting the integrity of the other A, C, and G nucleobases.
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Affiliation(s)
- Nicolas Probst
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Rémy Lartia
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Océane Théry
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Mouâd Alami
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Eric Defrancq
- University Grenoble-Alpes, DCM, CS 40700, 38058, Grenoble, France
| | - Samir Messaoudi
- BioCIS, Univ. Paris-Sud, CNRS, University Paris-Saclay, 92290, Châtenay-Malabry, France
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5
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Gong L. Analysis of oligonucleotides by ion-pairing hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:2125-2134. [PMID: 28972295 DOI: 10.1002/rcm.8004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry (HILIC-LC/ESI-MS) has been proved to be useful for the quality control of oligonucleotides. However, the lack of separation for some oligonucleotides using HILIC-LC/MS has proved problematic. This study aimed to improve the resolving ability of HILIC-LC/MS. METHODS The study was performed on a Waters UPLC® system coupled to a Waters LCT premier XE ESI-TOF mass spectrometer using a Zorbax® RRHD HILIC column (2.1 mm × 100 mm, 1.8 μm). Buffer systems contained triethylammonium acetate (TEAA) and acetonitrile. The effects of the concentration of TEAA and the type of organic modifiers on the separation of oligonucleotides were investigated. RESULTS The results showed that the optimum concentration of TEAA is 10 mM and acetonitrile is a better organic solvent than methanol. The addition of TEAA in the HILIC mobile phase improved the separation of N from N + A significantly compared to the HILIC method buffered with ammonium acetate. The IP-HILIC chromatography has demonstrated that the separation of oligonucleotides is sequence dependent. In addition, the IP-HILIC method produces a much simpler mass spectrum of an oligonucleotide with very efficient desalting. CONCLUSIONS The HILIC-LC/MS method with the addition of TEAA at a MS-compatible concentration has improved the separation of oligonucleotides. The IP-HILIC-LC/MS method also produces very simple mass spectra with high desalting efficiency.
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Affiliation(s)
- Lingzhi Gong
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Estalayo-Adriàn S, Lartia R, Meyer A, Vasseur JJ, Morvan F, Defrancq E. Assessment of the Full Compatibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition and Oxime Click Reactions for bis-Labelling of Oligonucleotides. ChemistryOpen 2014; 4:169-73. [PMID: 25969815 PMCID: PMC4420589 DOI: 10.1002/open.201402099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 12/23/2022] Open
Abstract
The conjugation of oligonucleotides with reporters is of great interest for improving their intrinsic properties or endowing new ones. In this context, we report herein a new procedure for the bis-labelling of oligonucleotides through oxime ligation (Click-O) and copper(I)-catalyzed alkyne–azide cycloaddition (Click-H). 5′-Azido and 3′-aldehyde precursors were incorporated into oligonucleotides, and subsequent coupling reactions through Click-O and Click-H (or vice versa) were successfully achieved. In particular, we exhaustively investigated the full compatibility of each required step for both tethering strategies. The results demonstrate that click Huisgen and click oxime reactions are fully compatible. However, whilst both approaches can deliver the targeted doubly conjugated oligonucleotide, the route involving click oxime ligation prior to click Huisgen is significantly more successful. Thus the reactions investigated here can be considered to be key elements of the chemical toolbox for the synthesis of highly sophisticated bioconjugates.
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Affiliation(s)
- Sandra Estalayo-Adriàn
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
| | - Rémy Lartia
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - Eric Defrancq
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
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7
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Sista P, Ghosh K, Martinez JS, Rocha RC. Metallo-Biopolymers: Conjugation Strategies and Applications. POLYM REV 2014. [DOI: 10.1080/15583724.2014.913063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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8
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Gong L, McCullagh JSO. Comparing ion-pairing reagents and sample dissolution solvents for ion-pairing reversed-phase liquid chromatography/electrospray ionization mass spectrometry analysis of oligonucleotides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:339-350. [PMID: 24395501 DOI: 10.1002/rcm.6773] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/19/2013] [Accepted: 10/20/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE A sensitive and selective liquid chromatography/mass spectrometry (LC/MS) method is essential for quality control of synthetic oligonucleotides. However, researchers are still searching for improvements to ion-pairing reagents for ion-pairing reversed-phase LC/MS. This study performed a comprehensive comparison of six ion-pairing reagents to determine their performance as mobile phase modifiers for oligonucleotide LC/MS. METHODS The study was performed using a Waters ultra-performance liquid chromatography (UPLC®) system coupled to a Waters LCT premier XE ESI-TOF mass spectrometer by using a UPLC® OST column (2.1 mm × 100 mm, 1.7 µm). Buffer systems containing ion-pairing reagents (triethylamine, tripropylamine, hexylamine, N,N-dimethylbutylamine, dibutylamine, N,N-diisopropylethylamine) and hexafluoro-2-propanol were compared by measuring the adduct ion formation, chromatographic separation, and MS signal intensity of four oligonucleotides (10mer to 40mer). The effect of dissolution solvents on MS signal intensity and adduct ion formation was also investigated. RESULTS Results showed that the type of dissolution solvent can have a signficiant impact on adduct ion formation with oligonucleotides. Results also showed that the maximum separation for small, medium and large oligonucleotides occured when using tripropylamine, N,N-dimethylbutylamine, and dibutylamine, respectively. However, on average 15 mM hexylamine and 50 mM hexafluoro-2-propanol provided the best chromtatographic performance (resolution values: 14.1 ± 0.34, 11.0 ± 0.17, and 6.4 ± 0.11 for the pairs of oligonucleotides T10 & T15, T15 & T25, and T25 & T40, respectively (3 replicates)). CONCLUSIONS The impact of dissolution solvent on the MS signal of oligonucleotides depends on the type of ion-pairing reagent. Buffer combining 15 mM hexylamine and 50 mM hexafluoro-2-propanol produced the highest overall performance for oligonucleotides (10mer to 40mer) with respect to chromatographic resolution and mass detection.
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Affiliation(s)
- Lingzhi Gong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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9
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Viault G, Dautrey S, Maindron N, Hardouin J, Renard PY, Romieu A. The first "ready-to-use" benzene-based heterotrifunctional cross-linker for multiple bioconjugation. Org Biomol Chem 2013; 11:2693-705. [PMID: 23474872 DOI: 10.1039/c3ob40086g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The synthesis and applications of the first water-soluble benzene derivative bearing a set of three different and orthogonal bioconjugatable groups (aminooxy, azido and thiol) are described. The combined use of a 5-amino isophthalic acid scaffold and unusual acid-labile protecting groups for temporarily masking aminooxy and thiol moieties has enabled the development of a highly convergent approach towards the synthesis of such a trivalent bioconjugation platform in good yields. The potential utility of this "ready-to-use" cross-linking reagent for creating complex and fragile tri-component (bio)molecular systems was illustrated through (1) the rapid preparation of a three-colour FRET cascade with valuable spectral properties and (2) the luminescent/fluorescent labelling of peptides and peptide-oligonucleotide conjugates. Thus, such (bio)molecular assemblies were readily obtained via a three-step process or in a "one-pot" manner, both involving oxime ligation, thiol-alkylation (S(N)2 or Michael addition) and copper-catalysed azide-alkyne 1,3-dipolar cycloaddition (CuAAC) reactions.
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Affiliation(s)
- Guillaume Viault
- Normandie Univ, COBRA, UMR 6014 & FR 3038, UNIV Rouen, INSA Rouen, CNRS, 1 Rue Tesnières, 76821 Mont St Aignan Cedex, France
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10
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Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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Moreau J, Dendane N, Schöllhorn B, Spinelli N, Fave C, Defrancq E. Synthesis and characterization of oligonucleotide conjugates bearing electroactive labels. Bioorg Med Chem Lett 2012; 23:955-8. [PMID: 23324407 DOI: 10.1016/j.bmcl.2012.12.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/12/2012] [Accepted: 12/15/2012] [Indexed: 12/16/2022]
Abstract
Oxime bond formation has been applied to the preparation of oligonucleotides labeled with electrochemical ferrocene and viologen labels. Aminooxy functionalized ferrocene and viologen derivatives were prepared by a straightforward route and efficiently conjugated with aldehyde containing oligonucleotides either at 3' or 5' end. Both labels were found to not disturb the recognition properties of the oligonucleotide. The versatility of the method was further demonstrated by preparing bi-functionalized conjugates with a disulfide at 3' end and an electrochemical label at 5' end.
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Affiliation(s)
- Julie Moreau
- Institut de Topologie et de Dynamique des Systèmes, UMR 7086 CNRS/Université Paris Diderot, Sorbonne Paris Cité, 15 rue Jean-Antoine de Baïf, 75205 Paris Cedex, France
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12
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Wenjuan Y, Le Goff A, Spinelli N, Holzinger M, Diao GW, Shan D, Defrancq E, Cosnier S. Electrogenerated trisbipyridyl Ru(II)-/nitrilotriacetic-polypyrene copolymer for the easy fabrication of label-free photoelectrochemical immunosensor and aptasensor: application to the determination of thrombin and anti-cholera toxin antibody. Biosens Bioelectron 2012; 42:556-62. [PMID: 23261689 DOI: 10.1016/j.bios.2012.11.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/10/2012] [Accepted: 11/12/2012] [Indexed: 11/16/2022]
Abstract
A bifunctional copolymer was electrogenerated, which allows efficient bioreceptor immobilization and transduction of the biorecognition event. This copolymer was formed using pyrenebutyric acid Nα',Nα-bis(carboxymethyl)-L-lysine amide (NTA-pyrene) and [tris-(2,2'-bipyridine) (4,4'-bis(4-pyrenyl-1-ylbutyloxy)-2,2'-bipyridine] ruthenium(II) hexafluorophosphate (Ru(II)-pyrene) complex. The pyrene groups, present in both compounds, undergo oxidative electropolymerization on platinum electrodes. The resulting copolymer contains NTA moieties, which were used as a versatile immobilization system for biotin- and histidine-tagged biomolecules, while Ru(II)-pyrene was employed as a photoelectrochemical transducing molecule. The efficiency of this copolymer for biomolecule anchoring was investigated with biotin- and histidine- tagged glucose oxidases, biotin-tagged cholera toxin and a histidine-tagged thrombin aptamer. The constructed enzyme electrodes exhibited an amperometric response toward glucose at 0.6 V vs SCE, demonstrating the anchoring of this enzyme via two coordination systems. An immunosensor configuration based on the immobilization of biotin-tagged cholera toxin was applied to the detection of anti-cholera antibody while the aptasensor based on the immobilization of histidine-tagged thrombin aptamer was tested for thrombin determination. The biorecognition events were monitored via the evolution of the photocurrent intensity generated by the polymerized Ru(II)-pyrene in the presence of visible light and a sacrificial donor (ascorbate). The binding of the targets hinders the diffusion of the sacrificial donor, inducing thus a photocurrent decrease. The constructed immunosensor presents a specific label-free photoelectrochemical response to anti-cholera antibody without labeling step, the detection limit being 0.2 μg mL⁻¹. The label-free photoelectrochemical response of the aptasensor varies linearly with thrombin concentrations up to 10 pmol L⁻¹, the detection limit being 1×10⁻¹³ mol L⁻¹.
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Affiliation(s)
- Yao Wenjuan
- Département de Chimie Moléculaire, Université Joseph Fourier, UMR-5250, ICMG FR-2607, CNRS, Grenoble, France
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13
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Xu H, Gorgy K, Gondran C, Le Goff A, Spinelli N, Lopez C, Defrancq E, Cosnier S. Label-free impedimetric thrombin sensor based on poly(pyrrole-nitrilotriacetic acid)-aptamer film. Biosens Bioelectron 2012; 41:90-5. [PMID: 22959014 DOI: 10.1016/j.bios.2012.07.044] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/21/2012] [Accepted: 07/23/2012] [Indexed: 11/15/2022]
Abstract
A label-free and highly sensitive impedimetric aptasensor was developed based on electropolymerized film for the determination of thrombin. The first step is the electrogeneration of a poly(pyrrole-nitrilotriacetic acid) (poly(pyrrole-NTA)) film onto the surface of electrodes followed by complexation of Cu(2+) ions. Then, the histidine labeled thrombin aptamer was immobilized onto the electrode through coordination of the histidine groups on the NTA-Cu(2+) complex. The aptamer sensor was applied for the detection and quantification of thrombin via impedimetric detection without a labeling step. A linear quantification of thrombin was obtained in the range 4.7×10(-12)-5.0×10(-10) mol L(-1) with a sensitivity of 2838 Ω/log unit (R(2)=0.9984). The impedance modulus at 0.3 Hz as a function of thrombin concentration was used to elaborate a similar linear relationship from 4.7×10(-12) to 5×10(-10) mol L(-1). In addition, aptamer-poly(pyrrole-NTA) electrodes incubated for 40 min in aqueous solutions of bovine serum albumin (BSA), lysozyme and IgG (5×10(-7) mol L(-1)) did not exhibit non-specific adsorption of proteins. Moreover, it has been demonstrated that the selective sensor can be regenerated several times with a good reproducibility.
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Affiliation(s)
- Hui Xu
- Département de Chimie Moléculaire, UMR-5250, ICMG FR-2607, CNRS, Université Joseph Fourier BP 53, 38041 Grenoble Cédex 9, France
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14
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Morvan F, Vidal S, Souteyrand E, Chevolot Y, Vasseur JJ. DNA glycoclusters and DNA-based carbohydrate microarrays: From design to applications. RSC Adv 2012. [DOI: 10.1039/c2ra21550k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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15
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Bonnet R, Murat P, Spinelli N, Defrancq E. Click–click chemistry on a peptidic scaffold for easy access to tetrameric DNA structures. Chem Commun (Camb) 2012; 48:5992-4. [DOI: 10.1039/c2cc32010j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Ghesquière J, Gauthier N, De Winter J, Gerbaux P, Moucheron C, Defrancq E, Kirsch-De Mesmaeker A. Photocrosslinking between peptide-peptide or peptide-oligonucleotide by Ru(II)-TAP complexes. Chemistry 2011; 18:355-64. [PMID: 22139993 DOI: 10.1002/chem.201101458] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Indexed: 01/23/2023]
Abstract
Ru(II)-TAP complexes have been shown to be very attractive compounds in the frame of developments of new anticancer drugs targeting the genetic material. This increasing interest originates from observations of covalent bond formations, triggered by photo-induced electron transfer (PET) between Ru(II)-TAP complexes and guanine bases of DNA. This photoreaction has recently been extended to the tryptophan (Trp) amino acid for future applications involving peptides. Thus, a double photo-addition of Trp residues of peptides on Ru(II) complexes is demonstrated by mass spectrometry with some structural issues. Such bi-adduct formations offer the possibility of photocrosslinking two Trp-containing biomolecules, which is investigated in this study. Thus, photocrosslinking between two complementary oligonucleotides (ODNs) derivatized by Trp-containing tripeptides is demonstrated by polyacrylamide gel electrophoresis (PAGE) in the presence of Ru(II)-TAP complexes. Both PAGE and MS indicate that such photocrosslinkings arise from two reaction pathways: either via the double addition of Trp residues on the Ru complex or from dimerization of Trp radicals. The competition between these two pathways depends on the experimental conditions. Heterobridgings between guanine bases and tryptophan residues mediated by Ru(II)-TAP complexes is also examined, opening the way to ODN-peptide photocrosslinkings.
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Affiliation(s)
- Jonathan Ghesquière
- Service de Chimie Organique et Photochimie, Université Libre de Bruxelles, 50 Av. F. D. Roosevelt, B-1050 Bruxelles, Belgium
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17
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Tuccitto N, Giamblanco N, Ghosh S, Spampinato V, Labbé P, Dumy P, Quici S, Marletta G, Defrancq E, Licciardello A. Controlled density patterning of tolylterpyridine-tagged oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:8595-8599. [PMID: 21682261 DOI: 10.1021/la2003468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
An efficient surface anchoring strategy of tolylterpyridine-tagged DNA single strands (ssDNA-ttpy) synthesized on gold electrodes is reported. The method is based on exchange reactions between Fe(II)bis-terpyridine complexed SAMs and ssDNA-ttpy, and allows efficient hybrydization of the cDNA strands. Moreover, by using low-current focused ion beam lithography, micropatterned arrays are obtained, homogeneously covered with ssDNA-ttpy. The surface adsorption kinetics of ssDNA-ttpy, as well as its hybridization efficiency, was monitored by in situ quartz crystal microbalance with dissipation monitoring (QCM-D) technique. The effective confinement of the ssDNA-ttpy at the micrometer level has been monitored by time of flight secondary ion mass spectrometry (ToF-SIMS) and ellipsometric surface imaging experiments, providing laterally resolved chemical and topographic mapping.
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Affiliation(s)
- Nunzio Tuccitto
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN), Dipartimento di Scienze Chimiche, Università degli Studi di Catania and CSGI, Catania, Italy
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Abstract
Integrins have become key targets for molecular imaging and for selective delivery of anti-cancer agents. Here we review recent work concerning the targeted delivery of antisense and siRNA oligonucleotides via integrins. A variety of approaches have been used to link oligonucleotides to ligands capable of binding integrins with high specificity and affinity. This includes direct chemical conjugation, incorporating oligonucleotides into lipoplexes, and use of various polymeric nanocarriers including dendrimers. The ligand-oligonucleotide conjugate or complex associates selectively with the integrin, followed by internalization into endosomes and trafficking through subcellular compartments. Escape of antisense or siRNA from the endosome to the cytosol and nucleus may come about through endogenous trafficking mechanisms, or because of membrane disrupting capabilities built into the conjugate or complex. Thus a variety of useful strategies are available for using integrins to enhance the pharmacological efficacy of therapeutic oligonucleotides.
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19
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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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20
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Bencini A, Lippolis V. 1,10-Phenanthroline: A versatile building block for the construction of ligands for various purposes. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.04.008] [Citation(s) in RCA: 288] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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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: 74] [Impact Index Per Article: 5.3] [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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22
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Baur J, Gondran C, Holzinger M, Defrancq E, Perrot H, Cosnier S. Label-Free Femtomolar Detection of Target DNA by Impedimetric DNA Sensor Based on Poly(pyrrole-nitrilotriacetic acid) Film. Anal Chem 2009; 82:1066-72. [DOI: 10.1021/ac9024329] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jessica Baur
- Département de Chimie Moléculaire, UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier Grenoble I, BP 53, 38041 Grenoble cedex 9, France, and Laboratoire Interfaces et Systèmes Electrochimiques, UPR 15 CNRS, Université Pierre et Marie Curie Paris VI, cpr 133, 75252 Paris cedex 05, France
| | - Chantal Gondran
- Département de Chimie Moléculaire, UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier Grenoble I, BP 53, 38041 Grenoble cedex 9, France, and Laboratoire Interfaces et Systèmes Electrochimiques, UPR 15 CNRS, Université Pierre et Marie Curie Paris VI, cpr 133, 75252 Paris cedex 05, France
| | - Michael Holzinger
- Département de Chimie Moléculaire, UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier Grenoble I, BP 53, 38041 Grenoble cedex 9, France, and Laboratoire Interfaces et Systèmes Electrochimiques, UPR 15 CNRS, Université Pierre et Marie Curie Paris VI, cpr 133, 75252 Paris cedex 05, France
| | - Eric Defrancq
- Département de Chimie Moléculaire, UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier Grenoble I, BP 53, 38041 Grenoble cedex 9, France, and Laboratoire Interfaces et Systèmes Electrochimiques, UPR 15 CNRS, Université Pierre et Marie Curie Paris VI, cpr 133, 75252 Paris cedex 05, France
| | - Hubert Perrot
- Département de Chimie Moléculaire, UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier Grenoble I, BP 53, 38041 Grenoble cedex 9, France, and Laboratoire Interfaces et Systèmes Electrochimiques, UPR 15 CNRS, Université Pierre et Marie Curie Paris VI, cpr 133, 75252 Paris cedex 05, France
| | - Serge Cosnier
- Département de Chimie Moléculaire, UMR 5250, ICMG FR 2607, CNRS, Université Joseph Fourier Grenoble I, BP 53, 38041 Grenoble cedex 9, France, and Laboratoire Interfaces et Systèmes Electrochimiques, UPR 15 CNRS, Université Pierre et Marie Curie Paris VI, cpr 133, 75252 Paris cedex 05, France
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23
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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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24
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Ghosh S, Pignot-Paintrand I, Dumy P, Defrancq E. Design and synthesis of novel hybrid metal complex-DNA conjugates: key building blocks for multimetallic linear DNA nanoarrays. Org Biomol Chem 2009; 7:2729-37. [PMID: 19532989 DOI: 10.1039/b904758a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe here a short and efficient synthetic route for incorporating terpyridine based metal complexes at the 3'-extremity of both single and bis-oligonucleotide (bis-ODN) stretches to form novel metal complex-ODN conjugates. All single stranded mono and bis-ODN tethered metal complexes and the respective duplex ODNs were characterized by circular dichroism spectroscopy and UV-Vis melting experiments. Duplexes formed by these hybrid metal complex-DNA conjugates showed around 4-5 degrees C stabilization with respect to the unmodified duplexes. Moreover hybridization of two complementary bis-ODN tethered metal complexes at different ratios in solution gave rise to a self-assembled nanometric linear network, which was characterized by non-denaturing gel electrophoresis and TEM studies. Thus, our simple synthetic strategy would contribute to develop multimetallic 2D-DNA nanoarrays where we can place different metal complexes at regular intervals along the ODN stretches.
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Affiliation(s)
- Sumana Ghosh
- Département de Chimie Moléculaire UMR CNRS 5250, Université Joseph Fourier BP 53, 38041, Grenoble Cedex 9, France
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25
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Murat P, Cressend D, Spinelli N, Van der Heyden A, Labbé P, Dumy P, Defrancq E. A novel conformationally constrained parallel g quadruplex. Chembiochem 2009; 9:2588-91. [PMID: 18821555 DOI: 10.1002/cbic.200800457] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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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26
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Richard A, Barras A, Younes AB, Monfilliette-Dupont N, Melnyk P. Minimal Chemical Modification of Reductive End of Dextran to Produce an Amphiphilic Polysaccharide Able to Incorporate onto Lipid Nanocapsules. Bioconjug Chem 2008; 19:1491-5. [DOI: 10.1021/bc700444t] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Antoine Richard
- Laboratoire de Chimie et MicroNanotechnologie à Visée Thérapeutique, UMR 8161 CNRS-Université de Lille 2-Université de Lille 1-Institut Pasteur de Lille, and INSERM IFR 142 Institut Pasteur de Lille-Institut de Biologie de Lille, Institut de Biologie de Lille, 1 Rue du Pr. Calmette, 59021 Lille cedex, France
| | - Alexandre Barras
- Laboratoire de Chimie et MicroNanotechnologie à Visée Thérapeutique, UMR 8161 CNRS-Université de Lille 2-Université de Lille 1-Institut Pasteur de Lille, and INSERM IFR 142 Institut Pasteur de Lille-Institut de Biologie de Lille, Institut de Biologie de Lille, 1 Rue du Pr. Calmette, 59021 Lille cedex, France
| | - Amena Ben Younes
- Laboratoire de Chimie et MicroNanotechnologie à Visée Thérapeutique, UMR 8161 CNRS-Université de Lille 2-Université de Lille 1-Institut Pasteur de Lille, and INSERM IFR 142 Institut Pasteur de Lille-Institut de Biologie de Lille, Institut de Biologie de Lille, 1 Rue du Pr. Calmette, 59021 Lille cedex, France
| | - Nicole Monfilliette-Dupont
- Laboratoire de Chimie et MicroNanotechnologie à Visée Thérapeutique, UMR 8161 CNRS-Université de Lille 2-Université de Lille 1-Institut Pasteur de Lille, and INSERM IFR 142 Institut Pasteur de Lille-Institut de Biologie de Lille, Institut de Biologie de Lille, 1 Rue du Pr. Calmette, 59021 Lille cedex, France
| | - Patricia Melnyk
- Laboratoire de Chimie et MicroNanotechnologie à Visée Thérapeutique, UMR 8161 CNRS-Université de Lille 2-Université de Lille 1-Institut Pasteur de Lille, and INSERM IFR 142 Institut Pasteur de Lille-Institut de Biologie de Lille, Institut de Biologie de Lille, 1 Rue du Pr. Calmette, 59021 Lille cedex, France
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27
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Spinelli N, Singh Y, Defrancq E, Dumy P. Aldehydic oligonucleotide: a key intermediate for the preparation of oligonucleotide conjugates through oxime bond formation. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:883-7. [PMID: 18058501 DOI: 10.1080/15257770701505436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Oligonucleotides functionalized with an aldehyde group are the key intermediates used for the preparation of peptide-oligonucleotide conjugates through the formation of an oxime linkage. Herein, we describe a brief overview of various synthetic protocols developed in our laboratory for the preparation of aldehyde containing oligonucleotides and their subsequent conjugation with peptides.
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Affiliation(s)
- N Spinelli
- Département de Chimie Moléculaire-UMR CNRS 5250, ICMG FR2607, Université Joseph Fourier, Grenoble, Cedex 9, France
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28
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Boturyn D, Defrancq E, Dolphin GT, Garcia J, Labbe P, Renaudet O, Dumy P. RAFT Nano-constructs: surfing to biological applications. J Pept Sci 2008; 14:224-40. [DOI: 10.1002/psc.964] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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The oxime bond formation as an efficient tool for the conjugation of ruthenium complexes to oligonucleotides and peptides. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.08.088] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Spinelli N, Edupuganti OP, Defrancq E, Dumy P. New solid support for the synthesis of 3'-oligonucleotide conjugates through glyoxylic oxime bond formation. Org Lett 2007; 9:219-22. [PMID: 17217269 DOI: 10.1021/ol062607b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel solid support 1 was synthesized to incorporate glyoxylic aldehyde functionality at the oligonucleotide 3'-terminus. 6-mer and 11-mer oligonucleotide sequences containing 3'-glyoxylic aldehyde functionality were prepared by using this support. These modified oligonucleotides were coupled to reporters containing an aminooxy group to prepare oligonucleotide 3'-conjugates through glyoxylic oxime bond formation. The hydrolytic stability of a glyoxylic oxime linkage was also investigated. [reaction: see text].
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Affiliation(s)
- Nicolas Spinelli
- Département de Chimie Moléculaire, UMR CNRS 5250, ICMG FR2607, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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31
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Yan H, Tram K. Glycotargeting to improve cellular delivery efficiency of nucleic acids. Glycoconj J 2007; 24:107-23. [PMID: 17268860 DOI: 10.1007/s10719-006-9023-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 11/07/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
Nucleic acids bearing glycans of various structures have been under vigorous investigation in the past decade. The carbohydrate moieties of such complexes can serve as recognition sites for carbohydrate-binding proteins-lectins-and initiate receptor-mediated endocytosis. Therefore, carbohydrates can enhance cell targeting and internalization of nucleic acids that are associated with them and thus improve the bioavailability of nucleic acids as therapeutic agents. This review summarizes nucleic acid glycosylation in nature and approaches for the preparation of both non-covalently associated and covalently-linked carbohydrate-nucleic acid complexes.
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Affiliation(s)
- Hongbin Yan
- Department of Chemistry, Brock University, 500 Glenridge Ave., St. Catharines, ON, Canada.
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32
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Chillemi R, Aleo D, Granata G, Sciuto S. Synthesis of very short chain lysophosphatidyloligodeoxynucleotides. Bioconjug Chem 2006; 17:1022-9. [PMID: 16848411 DOI: 10.1021/bc050365e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Very short chain 5'-O-lysophosphatidyloligonucleotides [5'-O-(1-O-palmitoyl-sn-glycero-3-phosphoryl)oligodeoxynucleotides, (5'-LyPOdNs)] were synthesized following a two-step chemoenzymatic synthesis. 5'-O-(sn-Glycero-3-phosphoryl)oligodeoxynucleotides (5'-GPOdNs) were first prepared by simply using a phosphoramidite of [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methanol (1) in a further coupling step after the solid-phase elongation of each desired oligodeoxynucleotide. Next, the regioselective palmitoylation at the C-1 hydroxyl of the glycerol moiety of 5'-GPOdNs was achieved by a lipase-catalyzed transacylation with trifluoroethyl palmitate in organic solvent. Despite of the molecular bulkiness of 5'-GPOdNs, 2-, 3-, and 4-mer 5'-LyPOdNs were prepared by this procedure. Although in very low yield, 5- and 6-mer 5'-LyPOdNs were also obtained by this way.
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Affiliation(s)
- Rosa Chillemi
- Dipartimento di Scienze Chimiche, Università di Catania, viale A. Doria 6, 95125, Catania, Italy
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33
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Singh Y, Dolphin GT, Razkin J, Dumy P. Synthetic Peptide Templates for Molecular Recognition: Recent Advances and Applications. Chembiochem 2006; 7:1298-314. [PMID: 16892470 DOI: 10.1002/cbic.200600078] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The creation of molecular systems that can mimic some of the properties of natural macromolecules is one of the major endeavors in contemporary protein chemistry. However, the construction of artificial proteins with predetermined structure and function is difficult on account of complex folding pathways. The use of topological peptide templates has been suggested to induce and stabilize defined secondary and tertiary structures. This is because the recent advances in the chemistry of coupling reagents, protecting groups, and solid-phase synthesis have made the chemical synthesis of peptides with conformationally controlled and complex structures feasible. Besides their use as structure-inducing devices, these peptide templates can also be utilized to construct novel structures with tailor-made functions. Herein, we present recent advances in the field of peptide-template-based approaches with particular emphasis on the demonstrated utility of this approach in molecular recognition, along with related applications.
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Affiliation(s)
- Yashveer Singh
- LEDSS, UMR CNRS 5616, ICMG FR 2607, Universite Joseph Fourier, Grenoble Cedex 9, France
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34
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Singh Y, Spinelli N, Defrancq E, Dumy P. A novel heterobifunctional linker for facile access to bioconjugates. Org Biomol Chem 2006; 4:1413-9. [PMID: 16557331 DOI: 10.1039/b518151h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A convenient synthesis of a novel heterobifunctional linker molecule is described. The linker contains a thiol-reactive nitropyridyl disulfide group (Npys) and an aldehyde-reactive aminooxy group with a propensity to form disulfide and oxime linkages. The utility of the linker molecule to cross-link different biomolecules has been demonstrated by employing it in the efficient preparation of a peptide-oligonucleotide conjugate. The linker reported herein could be a useful tool for cross-coupling of different but appropriately functionalised biomolecules.
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Affiliation(s)
- Yashveer Singh
- LEDSS, UMR CNRS 5616, ICMG FR 2607, Université Joseph Fourier, 301 rue de la Chimie, BP 53, F 38041, Grenoble Cedex 9, France
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35
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Garanger E, Boturyn D, Renaudet O, Defrancq E, Dumy P. Chemoselectively Addressable Template: A Valuable Tool for the Engineering of Molecular Conjugates. J Org Chem 2006; 71:2402-10. [PMID: 16526790 DOI: 10.1021/jo0525480] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We herein report the modular design and the synthesis of new molecular conjugates, which can combine a cell targeting function (ligand domain) with potential cytotoxic molecules (effector domain). The present approach utilizes a cyclic peptide template, Chemoselectively Addressable Template (CAT) as a key intermediate. These CAT molecules exhibit two independent and chemically addressable domains which permits the sequential and regioselective assembly of different ligand and/or effector domains. The attachment of various units to the template was achieved by the formation of iterative oxime bonds. The chemoselective oxime bonds were produced by the reaction of glyoxylyl aldehyde groups obtained from serine precursors. The process was further developed to prevent transoximation reactions. RAFT(c[-RGDfK-])4, a synthetic vector targeting the tumor-associated a alpha(V)beta3 integrin was prepared and coupled to either a cytotoxic peptide or oligonucleotide as an illustration of present approach. The potential application of this approach has been further demonstrated by the synthesis of high molecular weight compounds such as RAFT(c[-RGDfK-])16, a alpha(V)beta3-targeting ligand of high valency index.
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Affiliation(s)
- Elisabeth Garanger
- LEDSS, UMR CNRS 5616, ICMG FR-2607, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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36
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37
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Singh Y, Renaudet O, Defrancq E, Dumy P. Preparation of a multitopic glycopeptide-oligonucleotide conjugate. Org Lett 2006; 7:1359-62. [PMID: 15787506 DOI: 10.1021/ol050134n] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
[structure: see text] A novel strategy to prepare glycopeptide-oligonucleotide conjugates bearing a glycocluster is reported. The strategy utilizes a cyclodecapeptide scaffold as a key intermediate to anchor the carbohydrate cluster and the oligonucleotide through sequential oxime bond formation. The oligonucleotide glycocluster retains the binding affinity and recognition specificity for the target sequence. Furthermore, the conjugate shows enhanced binding to the specific lectins due to the cooperative effect produced by the carbohydrate cluster.
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Affiliation(s)
- Yashveer Singh
- LEDSS, UMR CNRS 5616, ICMG FR 2607, Université Joseph Fourier, BP 53, F 38041, Grenoble Cedex 9, France
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38
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Zatsepin TS, Stetsenko DA, Gait MJ, Oretskaya TS. Use of carbonyl group addition--elimination reactions for synthesis of nucleic acid conjugates. Bioconjug Chem 2005; 16:471-89. [PMID: 15898711 DOI: 10.1021/bc049712v] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This review outlines the synthesis of covalent conjugates of oligonucleotides and their analogues that are obtained by reactions of carbonyl compounds with various nucleophiles such as primary amines, N-alkoxyamines, hydrazines, and hydrazides. The products linked by imino, oxime, hydrazone, or thiazolidine groups are shown to be useful intermediates for a wide range of chemical biology applications. Methods for their preparation, isolation, purification, and analysis are highlighted, and the comparative stabilities of the respective linkages are evaluated. The relative merits of incorporation of a carbonyl group, particularly an aldehyde group, into either the oligonucleotide or the ligand parts are considered. Examples of harnessing of aldehyde-nucleophile coupling for the labeling of nucleic acids are given, as well as their conjugation to various biomolecules (e.g. peptides and small molecule ligands), site-specific cross-linking of oligonucleotides to nucleic acid-binding proteins, assembly of multibranched supramolecular structures, and immobilization on functionalized surfaces. Future perspectives of bioconjugation and complex molecular engineering via carbonyl group addition-elimination reactions in nucleic acids chemistry are discussed.
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Affiliation(s)
- Timofei S Zatsepin
- Department of Chemistry, M. V. Lomonossov Moscow State University, 1 Leninskie Gory, Moscow 119992, Russia
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39
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Kubler-Kielb J, Pozsgay V. A New Method for Conjugation of Carbohydrates to Proteins Using an Aminooxy-Thiol Heterobifunctional Linker. J Org Chem 2005; 70:6987-90. [PMID: 16095333 DOI: 10.1021/jo050934b] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new, efficient, and mild protocol is presented for the coupling of saccharides to proteins. First, a heterobifunctional aminooxy-thiol linker is coupled to the bromoacylated protein to introduce aminooxy groups through thioether linkages. Condensation of the aminooxylated protein and aldehydo/keto-derivatized carbohydrates affords covalent saccharide-protein constructs. Uncoupled saccharide can be recovered in its original form. The scope of our protocol is exemplified by the coupling of neutral mono- and tetrasaccharides and a negatively charged ribitol-phosphate construct to BSA.
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Affiliation(s)
- Joanna Kubler-Kielb
- National Institute of Child Health and Human Development, National Institutes of Health, 31 Center Drive, MSC 2423, Bethesda, MD 20892-2423, USA
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40
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Singh Y, Edupuganti OP, Villien M, Defrancq É, Dumy P. The oxime bond formation as a useful tool for the preparation of oligonucleotide conjugates. CR CHIM 2005. [DOI: 10.1016/j.crci.2005.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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