1
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Convenient Solid-Phase Attachment of Small-Molecule Ligands to Oligonucleotides via a Biodegradable Acid-Labile P-N-Bond. Molecules 2023; 28:molecules28041904. [PMID: 36838892 PMCID: PMC9961013 DOI: 10.3390/molecules28041904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
One of the key problems in the design of therapeutic and diagnostic oligonucleotides is the attachment of small-molecule ligands for targeted deliveries in such a manner that provides the controlled release of the oligonucleotide at a certain moment. Here, we propose a novel, convenient approach for attaching ligands to the 5'-end of the oligonucleotide via biodegradable, acid-labile phosphoramide linkage. The method includes the activation of the 5'-terminal phosphate of the fully protected, support-bound oligonucleotide, followed by interaction with a ligand bearing the primary amino group. This technique is simple to perform, allows for forcing the reaction to completion by adding excess soluble reactant, eliminates the problem of the limited solubility of reagents, and affords the possibility of using different solvents, including water/organic media. We demonstrated the advantages of this approach by synthesizing and characterizing a wide variety of oligonucleotide 5'-conjugates with different ligands, such as cholesterol, aliphatic oleylamine, and p-anisic acid. The developed method suits different types of oligonucleotides (deoxyribo-, 2'-O-methylribo-, ribo-, and others).
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2
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Novopashina DS, Semikolenova OA, Venyaminova AG. 5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches. Methods Mol Biol 2020; 2063:45-56. [PMID: 31667762 DOI: 10.1007/978-1-0716-0138-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.
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Affiliation(s)
- D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| | | | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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3
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Design, Synthesis and Molecular Modeling Study of Conjugates of ADP and Morpholino Nucleosides as A Novel Class of Inhibitors of PARP-1, PARP-2 and PARP-3. Int J Mol Sci 2019; 21:ijms21010214. [PMID: 31892271 PMCID: PMC6982223 DOI: 10.3390/ijms21010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
We report on the design, synthesis and molecular modeling study of conjugates of adenosine diphosphate (ADP) and morpholino nucleosides as potential selective inhibitors of poly(ADP-ribose)polymerases-1, 2 and 3. Sixteen dinucleoside pyrophosphates containing natural heterocyclic bases as well as 5-haloganeted pyrimidines, and mimicking a main substrate of these enzymes, nicotinamide adenine dinucleotide (NAD+)-molecule, have been synthesized in a high yield. Morpholino nucleosides have been tethered to the β-phosphate of ADP via a phosphoester or phosphoramide bond. Screening of the inhibiting properties of these derivatives on the autopoly(ADP-ribosyl)ation of PARP-1 and PARP-2 has shown that the effect depends upon the type of nucleobase as well as on the linkage between ADP and morpholino nucleoside. The 5-iodination of uracil and the introduction of the P–N bond in NAD+-mimetics have shown to increase inhibition properties. Structural modeling suggested that the P–N bond can stabilize the pyrophosphate group in active conformation due to the formation of an intramolecular hydrogen bond. The most active NAD+ analog against PARP-1 contained 5-iodouracil 2ʹ-aminomethylmorpholino nucleoside with IC50 126 ± 6 μM, while in the case of PARP-2 it was adenine 2ʹ-aminomethylmorpholino nucleoside (IC50 63 ± 10 μM). In silico analysis revealed that thymine and uracil-based NAD+ analogs were recognized as the NAD+-analog that targets the nicotinamide binding site. On the contrary, the adenine 2ʹ-aminomethylmorpholino nucleoside-based NAD+ analogs were predicted to identify as PAR-analogs that target the acceptor binding site of PARP-2, representing a novel molecular mechanism for selective PARP inhibition. This discovery opens a new avenue for the rational design of PARP-1/2 specific inhibitors.
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4
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Flamme M, Clarke E, Gasser G, Hollenstein M. Applications of Ruthenium Complexes Covalently Linked to Nucleic Acid Derivatives. Molecules 2018; 23:E1515. [PMID: 29932443 PMCID: PMC6099586 DOI: 10.3390/molecules23071515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 11/16/2022] Open
Abstract
Oligonucleotides are biopolymers that can be easily modified at various locations. Thereby, the attachment of metal complexes to nucleic acid derivatives has emerged as a common pathway to improve the understanding of biological processes or to steer oligonucleotides towards novel applications such as electron transfer or the construction of nanomaterials. Among the different metal complexes coupled to oligonucleotides, ruthenium complexes, have been extensively studied due to their remarkable properties. The resulting DNA-ruthenium bioconjugates have already demonstrated their potency in numerous applications. Consequently, this review focuses on the recent synthetic methods developed for the preparation of ruthenium complexes covalently linked to oligonucleotides. In addition, the usefulness of such conjugates will be highlighted and their applications from nanotechnologies to therapeutic purposes will be discussed.
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Affiliation(s)
- Marie Flamme
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Emma Clarke
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| | - Gilles Gasser
- Laboratory for Inorganic Chemical Biology, Chimie ParisTech, PSL University, F-75005 Paris, France.
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institute Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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5
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Tauraitė D, Jakubovska J, Dabužinskaitė J, Bratchikov M, Meškys R. Modified Nucleotides as Substrates of Terminal Deoxynucleotidyl Transferase. Molecules 2017; 22:molecules22040672. [PMID: 28441732 PMCID: PMC6154577 DOI: 10.3390/molecules22040672] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/10/2017] [Accepted: 04/19/2017] [Indexed: 11/30/2022] Open
Abstract
The synthesis of novel modified nucleotides and their incorporation into DNA sequences opens many possibilities to change the chemical properties of oligonucleotides (ONs), and, therefore, broaden the field of practical applications of modified DNA. The chemical synthesis of nucleotide derivatives, including ones bearing thio-, hydrazino-, cyano- and carboxy groups as well as 2-pyridone nucleobase-containing nucleotides was carried out. The prepared compounds were tested as substrates of terminal deoxynucleotidyl transferase (TdT). The nucleotides containing N4-aminocytosine, 4-thiouracil as well as 2-pyridone, 4-chloro- and 4-bromo-2-pyridone as a nucleobase were accepted by TdT, thus allowing enzymatic synthesis of 3’-terminally modified ONs. The successful UV-induced cross-linking of 4-thiouracil-containing ONs to TdT was carried out. Enzymatic post-synthetic 3’-modification of ONs with various photo- and chemically-reactive groups opens novel possibilities for future applications, especially in analysis of the mechanisms of polymerases and the development of photo-labels, sensors, and self-assembling structures.
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Affiliation(s)
- Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Julija Dabužinskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
| | - Maksim Bratchikov
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio g. 21, Vilnius LT-03101, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania.
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6
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Egloff D, Oleinich IA, Zhao M, König SLB, Sigel RKO, Freisinger E. Sequence-Specific Post-Synthetic Oligonucleotide Labeling for Single-Molecule Fluorescence Applications. ACS Chem Biol 2016; 11:2558-67. [PMID: 27409145 DOI: 10.1021/acschembio.6b00343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The sequence-specific fluorescence labeling of nucleic acids is a prerequisite for various methods including single-molecule Förster resonance energy transfer (smFRET) for the detailed study of nucleic acid folding and function. Such nucleic acid derivatives are commonly obtained by solid-phase methods; however, yields decrease rapidly with increasing length and restrict the practicability of this approach for long strands. Here, we report a new labeling strategy for the postsynthetic incorporation of a bioorthogonal group into single stranded regions of both DNA and RNA of unrestricted length. A 12-alkyne-etheno-adenine modification is sequence-selectively formed using DNA-templated synthesis, followed by conjugation of the fluorophore Cy3 via a copper-catalyzed azide-alkyne cycloaddition (CuAAC). Evaluation of the labeled strands in smFRET measurements shows that the strategy developed here has the potential to be used for the study of long functional nucleic acids by (single-molecule) fluorescence or other methods. To prove the universal use of the method, its application was successfully extended to the labeling of a short RNA single strand. As a proof-of-concept, also the labeling of a large RNA molecule in form of a 633 nucleotide long construct derived from the Saccharomyces cerevisiae group II intron Sc.ai5γ was performed, and covalent attachment of the Cy3 fluorophore was shown with gel electrophoresis.
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Affiliation(s)
- David Egloff
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Igor A. Oleinich
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Meng Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Sebastian L. B. König
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Roland K. O. Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
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7
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Vasilyeva SV, Filichev VV, Boutorine AS. Application of Cu(I)-catalyzed azide-alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA. Beilstein J Org Chem 2016; 12:1348-60. [PMID: 27559384 PMCID: PMC4979877 DOI: 10.3762/bjoc.12.128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/08/2016] [Indexed: 12/27/2022] Open
Abstract
Efficient protocols based on Cu(I)-catalyzed azide-alkyne cycloaddition were developed for the synthesis of conjugates of pyrrole-imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple helices by TFO-MGB conjugates was evaluated by gel-shift experiments. The presence of MGB in these conjugates did not affect the binding parameters (affinity and triplex stability) of the parent TFOs.
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Affiliation(s)
- Svetlana V Vasilyeva
- Institute of Chemical Biology & Fundamental Medicine, SB of RAS, pr. Lavrent’eva 8, 630090 Novosibirsk, Russia
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North, New Zealand
| | - Alexandre S Boutorine
- Structure and Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 57 rue Cuvier, C.P. 26, 75231 Paris cedex 05, France
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8
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Vigovskaya A, Abt D, Ahmed I, Niemeyer CM, Barner-Kowollik C, Fruk L. Photo-induced chemistry for the design of oligonucleotide conjugates and surfaces. J Mater Chem B 2016; 4:442-449. [DOI: 10.1039/c5tb02207j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A photocaged diene is introduced at the 5′-end of oligonucleotides using the H-phosphonate approach and subsequently employed for the light-induced conjugation to a protein and the spatially controlled immobilization onto surfaces.
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Affiliation(s)
- Antonina Vigovskaya
- DFG-Centre for Functional Nanostructures
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Institut für Biologische Grenzflächen
| | - Doris Abt
- Institut für Biologische Grenzflächen
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
- Preparative Macromolecular Chemistry
| | - Ishtiaq Ahmed
- Institut für Biologische Grenzflächen
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Christof M. Niemeyer
- Institut für Biologische Grenzflächen
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Christopher Barner-Kowollik
- Institut für Biologische Grenzflächen
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
- Preparative Macromolecular Chemistry
| | - Ljiljana Fruk
- DFG-Centre for Functional Nanostructures
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe
- Germany
- Department of Chemical Engineering and Biotechnology
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9
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Egloff D, Oleinich IA, Freisinger E. Sequence-specific generation of 1,N(6)-ethenoadenine and 3,N(4)-ethenocytosine in single-stranded unmodified DNA. ACS Chem Biol 2015; 10:547-53. [PMID: 25402665 DOI: 10.1021/cb500497p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA lesions such as 1,N(6)-ethenoadenine (εA) and 3,N(4)-ethenocytosine (εC) are ubiquitously present in genomes of different organisms and show increasing levels upon exposure to mutagenic substances or under conditions of chronic inflammations and infections. To facilitate investigations of the mutagenic properties and repair mechanisms of etheno-base adducts, access to oligonucleotides bearing these lesions at defined positions is of great advantage. In this study, we report a new synthetic strategy to sequence-specifically generate etheno-adducts in a single-stranded unmodified DNA sequence making use of a DNA-templated approach that positions the alkylating agent close in space to the respective target base. In contrast to solid-phase synthesis of modified oligonucleotides such DNA-templated methods can be applied to single-stranded nucleic acids of unrestricted lengths. The modular nature of the system allows straightforward adaptation to different sequences.
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Affiliation(s)
- David Egloff
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Igor A. Oleinich
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Eva Freisinger
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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10
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Novopashina DS, Siniakov AN, Riabinin VA, Perrouault L, Giovannangeli C, Venyaminova AG, Butorin AS. [Oligo(2'-O-Methylribonucleotides) and their derivatives: IV. Conjugates of oligo(2'-O-methylribonucleotides) with minor groove binders and intercalators: synthesis, properties and application]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:159-74. [PMID: 23964516 DOI: 10.1134/s1068162013010081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conjugates of pyrimidine triplex forming 3'-protected oligo(2'-O-methylribonucleotides) with minor groove binders (MGB) and triplex specific intercalator benzoindoloquinoline (BIQ) at 5'-terminus were synthesized. The conjugates formed stable complexes with target dsDNA by simultaneous binding both in its minor and major grooves and BIQ intercalation. The dissociation constants and thermal stability of the conjugate complexes with model dsDNA corresponding to polypurine tract (PPT) of genes nef and pol from HIV proviral genome were determined. Conjugation of oligo(2'-O-methylribonucleotides) with MGB and intercalator increased the stability of the triple complexes with dsDNA at pH 7.2 and 37 degrees C. Intercalator introduction accelerates the process of complex formation. Dose-dependent arrest of the in vitro transcription was demonstrated when a 780 b.p. DNA fragment containing the polypurine tract was transcribed under the control of T7 promoter in the presence of different concentrations of conjugates of oligo(2'-O-methylribonucleotides) containing MGB and BIQ intercalator.
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11
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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12
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Sallamand C, Miscioscia A, Lartia R, Defrancq E. Phosphorylating reagent-free synthesis of 5'-phosphate oligonucleotides by controlled oxidative degradation of their 5'-end. Org Lett 2012; 14:2030-3. [PMID: 22480332 DOI: 10.1021/ol300542s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 5'-phosphorylated oligonucleotides (5'-pONs) are currently synthesized using expensive and sensitive modified phosphoramidite reagents. In this work, a simple, cost-effective, efficient, and automatable method is presented, based on the controlled oxidation of the 5'-terminal alcohol followed by a β-elimination reaction. The latter reaction leads to the removal of the terminal 5'-nucleoside and subsequent formation of the 5'-phosphate moiety. Thus, chemical phosphorylation of oligonucleotides (DNA or RNA) is achieved without using modified phosphoramidites.
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Affiliation(s)
- Corinne Sallamand
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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13
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Beloglazova NG, Fabani MM, Polushin NN, Sil'nikov VV, Vlassov VV, Bichenkova EV, Zenkova MA. Site-selective artificial ribonucleases: oligonucleotide conjugates containing multiple imidazole residues in the catalytic domain. J Nucleic Acids 2011; 2011:748632. [PMID: 21961054 PMCID: PMC3180074 DOI: 10.4061/2011/748632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 07/05/2011] [Indexed: 12/05/2022] Open
Abstract
Design of site-selective artificial ribonucleases (aRNases) is one of the most challenging tasks in RNA targeting. Here, we designed and studied oligonucleotide-based aRNases containing multiple imidazole residues in the catalytic part and systematically varied structure of cleaving constructs. We demonstrated that the ribonuclease activity of the conjugates is strongly affected by the number of imidazole residues in the catalytic part, the length of a linker between the catalytic imidazole groups of the construct and the oligonucleotide, and the type of anchor group, connecting linker structure and the oligonucleotide. Molecular modeling of the most active aRNases showed that preferable orientation(s) of cleaving constructs strongly depend on the structure of the anchor group and length of the linker. The inclusion of deoxyribothymidine anchor group significantly reduced the probability of cleaving groups to locate near the cleavage site, presumably due to a stacking interaction with the neighbouring nucleotide residue. Altogether the obtained results show that dynamics factors play an important role in site-specific RNA cleavage. Remarkably high cleavage activity was displayed by the conjugates with the most flexible and extended cleaving construct, which presumably provides a better opportunity for imidazole residues to be correctly positioned in the vicinity of scissile phosphodiester bond.
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Affiliation(s)
- Natalia G Beloglazova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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14
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McKee ML, Evans AC, Gerrard SR, O'Reilly RK, Turberfield AJ, Stulz E. Peptidomimetic bond formation by DNA-templated acyl transfer. Org Biomol Chem 2011; 9:1661-6. [PMID: 21270981 DOI: 10.1039/c0ob00753f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The efficiencies of DNA-templated acyl transfer reactions between a thioester modified oligonucleotide and a series of amine and thiol based nucleophiles are directly compared. The reactivity of the nucleophile, reaction conditions (solvent, buffer, pH) and linker length all play important roles in determining the efficiency of the transfer reaction. Careful optimisation of the system enables the use of DNA-templated synthesis to form stable peptide-like bonds under mild aqueous conditions close to neutral pH.
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Affiliation(s)
- Mireya L McKee
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, United Kingdom OX1 3PU
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15
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Asseline U, Thuong NT. Modification of the 5' terminus of oligodeoxyribonucleotides for conjugation with ligands. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.9. [PMID: 18428856 DOI: 10.1002/0471142700.nc0409s05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Ligands can be introduced at the 5' terminus of an oligonucleotide by adding a linker to the ligand and modifying the 5' terminus of the oligonucleotide. These are then reacted to give the ligand-oligonucleotide conjugate. This unit describes the addition of carboxylated and aminoalkylated linkers, and phosphorothioate, phosphate, and masked thiol groups to the 5' terminus of an oligonucleotide. The addition of linkers to ligands and the final reaction that produces the ligand-conjugated oligonucleotide are described elsewhere in the series. This approach is particularly useful when there is a limited amount of ligand available, when the ligand is sensitive to chemical conditions required for oligonucleotide deprotection, or when the ligand is weakly soluble in solvents required for phosphoramidite- or H-phosphonate-mediated oligonucleotide synthesis.
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Affiliation(s)
- U Asseline
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
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16
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Abramova TV, Vasileva SV, Serpokrylova IY, Kless H, Silnikov VN. A facile and effective synthesis of dinucleotide 5'-triphosphates. Bioorg Med Chem 2007; 15:6549-55. [PMID: 17686631 DOI: 10.1016/j.bmc.2007.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 07/03/2007] [Accepted: 07/10/2007] [Indexed: 11/25/2022]
Abstract
We report on the successful synthetic procedure for the conversion of 5'-monophosphorylated 2'-deoxydinucleotides into their 5'-triphosphate derivatives in satisfactory to excellent yields. The activation of the terminal phosphate group was achieved under the Mukaiyama conditions in the presence of a nucleophilic catalyst. The reaction conditions (solvent, counter ions, activation time and reagent excess) were optimized for all dinucleotides.
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Affiliation(s)
- Tatiana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, Lavrent'ev Avenue, 8, Novosibirsk 630090, Russia.
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17
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Boutorine AS, Escudé C. Biophysical Analysis of Triple‐Helix Formation. ACTA ACUST UNITED AC 2007; Chapter 7:Unit 7.12. [DOI: 10.1002/0471142700.nc0712s29] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Novopashina DS, Sinyakov AN, Ryabinin VA, Venyaminova AG, Halby L, Sun JS, Boutorine AS. Sequence-specific conjugates of oligo(2'-O-methylribonucleotides) and hairpin oligocarboxamide minor-groove binders: design, synthesis, and binding studies with double-stranded DNA. Chem Biodivers 2007; 2:936-52. [PMID: 17193185 DOI: 10.1002/cbdv.200590071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
New conjugates of triplex-forming pyrimidine oligo(2'-O-methylribonucleotides) with one or two 'head-to-head' hairpin oligo(N-methylpyrrole carboxamide) minor-groove binders (MGBs) attached to the terminal phosphate of the oligonucleotides with a oligo(ethylene glycol) linker were synthesized. It was demonstrated that, under appropriate conditions, the conjugates form stable complexes with double-stranded DNA (dsDNA) similarly to triplex-forming oligo(deoxyribonucleotide) (TFO) conjugates containing 5-methylated cytosines. Kinetic and thermodynamic parameters of the complex formation were evaluated by gel-shift assay and thermal denaturation. Higher melting temperatures (Tm), faster complex formation, and lower dissociation constants (Kd) of the triple helices (6-7 nM) were observed for complexes of MGB-oligo(2'-O-methylribonucleotide) conjugates with the target dsDNA compared to the nonconjugated individual components. Interaction of MGB moieties with the HIV proviral DNA fragment was indicated by UV/VIS absorption changes at 320 nm in the melting curves. The introduction of thymidine via a 3',3'-type 'inverted' phosphodiester linkage at the 3'-end of oligo(2'-O-methylribonucleotide) conjugates (3'-protection) had no strong influence on triplex formation, but slightly affected complex stability. At pH 6.0, when one or two hairpin MGBs were attached to the oligonucleotide, both triplex formation and minor-groove binding played important roles in complex formation. When two 'head-to-head' oligo(N-methylpyrrole) ligands were attached to the same terminal phosphate of the oligonucleotide or the linker, binding was observed at pH >7.5 and at high temperatures (up to 74 degrees). However, under these conditions, binding was retained only by the MGB part of the conjugate.
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Affiliation(s)
- Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 8, 630090 Novosibirsk, Russia.
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Antsypovich SI, von Kiedrowski G. A novel versatile phosphoramidite building block for the synthesis of 5'- and 3'-hydrazide modified oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006; 24:211-26. [PMID: 15892260 DOI: 10.1081/ncn-55723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We introduce a novel versatile phosphoramidite building block for the modification of oligonucleotides (ONs) with acyl hydrazides on the 5'- or 3'-terminus, or both. The reaction of these hydrazide functionalized ONs with 4-methoxyphenylaldehyde is demonstrated for solution derivatization. Hydrazides are considered nowadays as promising reactants, which show enhanced reactivity at neutral and slightly acidic conditions and higher stability of yielding products as compared to the aliphatic amines, which are broadly used for ONs derivatization. Our method to introduce hydrazides into ONs employs a phosphoramidite modifier designed to split, during ammonia or lithium hydroxide treatment, into two hydrazides via beta-elimination of a central bis-2-carbonylethoxysulfone unit. It allows the creation of ONs derivatized with a hydrazide moiety at the 5'-, 3'- and both 5'- and 3'-termini, as well as two different hydrazide containing ONs at the same time, viz. in one sequence on the same solid support In latter case one can, for example, synthesize two hydrazide containing ONs, where one is 5'-modified and second one is 3'-modified.
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Duca M, Guianvarc'h D, Oussedik K, Halby L, Garbesi A, Dauzonne D, Monneret C, Osheroff N, Giovannangeli C, Arimondo PB. Molecular basis of the targeting of topoisomerase II-mediated DNA cleavage by VP16 derivatives conjugated to triplex-forming oligonucleotides. Nucleic Acids Res 2006; 34:1900-11. [PMID: 16598074 PMCID: PMC1447649 DOI: 10.1093/nar/gkl126] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human topoisomerase II (topo II) is the cellular target for a number of widely used antitumor agents, such as etoposide (VP16). These agents 'poison' the enzyme and induce it to generate DNA breaks that are lethal to the cell. Topo II-targeted drugs show a limited sequence preference, triggering double-stranded breaks throughout the genome. Circumstantial evidence strongly suggests that some of these breaks induce chromosomal translocations that lead to specific types of leukaemia (called treatment-related or secondary leukaemia). Therefore, efforts are ongoing to decrease these secondary effects. An interesting option is to increase the sequence-specificity of topo II-targeted drugs by attaching them to triplex-forming oligonucleotides (TFO) that bind to DNA in a highly sequence-specific manner. Here five derivatives of VP16 were attached to TFOs. The active topo II poisons, once linked, induced cleavage 13-14 bp from the triplex end where the drug was attached. The use of triple-helical DNA structures offers an efficient strategy for targeting topo II-mediated cleavage to DNA specific sequences. Finally, drug-TFO conjugates are useful tools to investigate the mechanistic details of topo II poisoning.
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Affiliation(s)
- Maria Duca
- UMR 5153 CNRSParis, France
- Muséum National d'Histoire Naturelle USM0503Paris, France
- INSERM UR565Paris, France
- 43 rue Cuvier75231 Paris cedex 05, France
| | - Dominique Guianvarc'h
- UMR 5153 CNRSParis, France
- Muséum National d'Histoire Naturelle USM0503Paris, France
- INSERM UR565Paris, France
- 43 rue Cuvier75231 Paris cedex 05, France
| | - Kahina Oussedik
- UMR 5153 CNRSParis, France
- Muséum National d'Histoire Naturelle USM0503Paris, France
- INSERM UR565Paris, France
- 43 rue Cuvier75231 Paris cedex 05, France
| | - Ludovic Halby
- UMR 5153 CNRSParis, France
- Muséum National d'Histoire Naturelle USM0503Paris, France
- INSERM UR565Paris, France
- 43 rue Cuvier75231 Paris cedex 05, France
| | - Anna Garbesi
- Istituto di Sintesi Organica e Fotoreattività del Consiglio Nazionale delle Ricerche (ISOF-CNR) Via Gobetti 10140129 Bologna, Italy
| | - Daniel Dauzonne
- UMR 176 CNRS, Institut Curie Section de Recherche26 rue d'Ulm 75248 Paris cedex 05, France
| | - Claude Monneret
- UMR 176 CNRS, Institut Curie Section de Recherche26 rue d'Ulm 75248 Paris cedex 05, France
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of MedicineNashville TN 37232-0146, USA
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of MedicineNashville TN 37232-0146, USA
| | - Carine Giovannangeli
- UMR 5153 CNRSParis, France
- Muséum National d'Histoire Naturelle USM0503Paris, France
- INSERM UR565Paris, France
- 43 rue Cuvier75231 Paris cedex 05, France
| | - Paola B. Arimondo
- UMR 5153 CNRSParis, France
- Muséum National d'Histoire Naturelle USM0503Paris, France
- INSERM UR565Paris, France
- 43 rue Cuvier75231 Paris cedex 05, France
- To whom correspondence should be addressed. Tel: +33 1 40793859; Fax: +33 1 40793705;
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Halby L, Ryabinin VA, Sinyakov AN, Boutorine AS. Functionalized head-to-head hairpin polyamides: Synthesis, double-stranded DNA-binding activity and affinity. Bioorg Med Chem Lett 2005; 15:3720-4. [PMID: 16005219 DOI: 10.1016/j.bmcl.2005.05.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 05/17/2005] [Accepted: 05/18/2005] [Indexed: 11/23/2022]
Abstract
A series of 4 functionalized head-to-head-linked hairpin oligo(N-methylpyrrole) carboxamides with different linkers have been synthesized. Their ability to bind double-stranded DNA and sequence specificity were compared and the apparent Kd values of their DNA complexes were determined. These compounds, particularly those with iminodiacetic linkers, revealed a high affinity for DNA (Kd = 4.5-4.8 x 10(-9) M) and sequence specific recognition of 9-10 base pairs.
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Affiliation(s)
- Ludovic Halby
- USM 0503-Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle, Paris, France
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Achilles K, Kiedrowski GV. Kinetic model studies on the chemical ligation of oligonucleotides via hydrazone formation. Bioorg Med Chem Lett 2005; 15:1229-33. [PMID: 15686948 DOI: 10.1016/j.bmcl.2004.11.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 11/23/2004] [Accepted: 11/25/2004] [Indexed: 11/27/2022]
Abstract
We report on the suitability of hydrazone formation for activator-free ligation of oligonucleotides. 5'-Acyl hydrazides were synthesized using a previously described phosphoramidite modifier, whereas 3'-hydrazides resulted from a hydrazinolysis of an ester group serving as a linker to the solid support. Aromatic aldehydes could be directly introduced on the 5'-terminus via the respective phosphoramidates. Aliphatic aldehydes were generated by periodate cleavage of the corresponding 3'- and 5'-modified diol precursors. Ligation of a 3'-hydrazide-modified oligonucleotide with oligonucleotides bearing an aromatic aldehyde in 5'-position showed a fast reaction kinetics (k(1) about 10(-1) M(-1)s(-1)) [corrected] and irreversible hydrazone formation. The ligation of a 5'-hydrazide-modified oligonucleotide and a 3'-ribobisaldehyde appeared to proceed reversibly at the beginning, but became irreversible with increasing reaction time. Hydrazide-modified oligonucleotides were found to be somewhat unstable in aqueous solutions.
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Affiliation(s)
- K Achilles
- Lehrstuhl für Organische Chemie I, Ruhr-Universität-Bochum, D-44780 Bochum, Germany
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Ryabinin VA, Boutorine AS, Hélène C, Denisov AY, Pyshnyi DV, Sinyakov AN. Oligonucleotide--minor groove binder 1:2 conjugates: side by side parallel minor groove binder motif in stabilization of DNA duplex. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:953-68. [PMID: 15560087 DOI: 10.1081/ncn-200026046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synthetic polycarboxamides consisting of N-methylpyrrole (Py), N-methylimidazole (Im), N-methyl-3-hydroxypyrrole (Hp) and beta-alanine (beta) show strong and sequence-specific interaction with the DNA minor groove when they form hairpin structures with side-by-side antiparallel motifs. In the present paper, new conjugates containing two ligands linked to the same terminal phosphate of DNA strand were constructed. The paper describes optimized synthesis and properties of oligonucleotide-linked polyamide strands that insert into the minor groove of a duplex in a parallel or antiparallel orientation. Strong stabilization of DNA duplexes by two attached minor groove ligands is demonstrated by the thermal denaturation method. The unmodified duplex 5'-CGTTTATTp-3'/5'-AATAAACG-3' melts at 20 degrees C. When one tetra(Py) residue was attached to the first strand of this duplex, denaturation temperature was increased to 46 degrees C; attachment of the second tetra(Py) in a parallel orientation resulted in denaturation temperature of 60 degrees C. It is even higher than in case of "classic" octapyrrole hairpin ligand (Tm = 58 degrees C). Sequence-specific character of stabilization by two conjugated ligands was demonstrated for G:C-containing oligonucleotides attached to tetracarboxamide and octacarboxamide ligands constructed from Py, Im and beta units according to established recognition rules (deltaTm = 20 degrees C). The two-strand parallel minor groove binder constructions attached to addressing oligonucleotides could be considered as site-specific ligands recognizing single- and double-stranded DNA similarly to already described hairpin MGB structures with antiparallel orientation of carboxamide units.
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Affiliation(s)
- Vladimir A Ryabinin
- Institute of Molecular Biology, State Research Center of Virology and Biotechnology "Vector," Novosibirsk Region, Kol'tsovo, Russia
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Novopashina DS, Sinyakov AN, Ryabinin VA, Venyaminova AG, Perrouault L, Brunet E, Giovannangeli C, Boutorine AS. Binding properties of the conjugates of oligo(2'-O-methylribonucleotides) with minor groove binders targeted to double stranded DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:1015-22. [PMID: 15560096 DOI: 10.1081/ncn-200026058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Design, synthesis, physico-chemical and in vitro biological studies of new pyrimidine oligo(2'-O-methylribonucleotide) conjugates with oligocarboxamide minor groove binders (MGB) and benzoindoloquinoline intercalator (BIQ) are described. These conjugates formed stable triple helices with the target double-stranded DNA and inhibited its in vitro transcription upon binding.
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Affiliation(s)
- D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.
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Effect of structural factors on the stability of duplexes formed by oligonucleotide conjugates with minor groove binders. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2005. [DOI: 10.1007/s11171-005-0020-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Ryabinin VA, Boutorine AS, Hélène C, Pyshnyi DV, Sinyakov AN. Oligonucleotide-minor groove binder conjugates and their complexes with complementary DNA: effect of conjugate structural factors on the thermal stability of duplexes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:789-803. [PMID: 15281367 DOI: 10.1081/ncn-120039358] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Synthetic polycarboxamide minor groove binders (MGB) consisting of N-methylpyrrole (Py), N-methylimidazole (Im), N-methyl-3-hydroxypyrrole (Hp) and beta-alanine (beta) show strong and sequence-specific interaction with the DNA minor groove in side-by-side antiparallel or parallel orientation. Two MGB moieties covalently linked to the same terminal phosphate of one DNA strand stabilize DNA duplexes formed by this strand with a complementary one in a sequence-specific manner, similarly to the corresponding mono-conjugated hairpin structures. The series of conjugates with the general formula Oligo-(L-MGB-R)m was synthesized, where m = 1 or 2, L = linker, R = terminal charged or neutral group, MGB = -(Py)n-, -(Im)n- or -[(Py/Im)n-(CH2)3CONH-(Py/Im)n-] and I < n < 5. Using thermal denaturation, we studied effects of structural factors such as m and n, linker L length, nature and orientation of the MGB monomers, the group R and the backbone (DNA or RNA), etc. on the stability of the duplexes. Structural factors are more important for linear and hairpin monophosphoroamidates than for parallel bis-phosphoroamidates. No more than two oligocarboxamide strands can be inserted into the duplex minor groove. Attachment of the second sequence-specific parallel ligand [-L(Py)4R] to monophosphoroamidate conjugate CGTTTATT-L(Py)4R leads to the increase of the duplex Tm, whereas attachment of [-L(Im)4R] leads to its decrease. The mode of interaction between oligonucleotide duplex and attached ligands could be different (stacking with the terminal A:T pair of the duplex or its insertion into the minor groove) depending on the length and structure of the MGB.
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Affiliation(s)
- Vladimir A Ryabinin
- State Research Center of Virology and Biotechnology Vector, Kol'tsovo, Institute of Molecular Biology, Novosibirsk Region, Russia
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Gosse C, Boutorine A, Aujard I, Chami M, Kononov A, Cogné-Laage E, Allemand JF, Li J, Jullien L. Micelles of Lipid−Oligonucleotide Conjugates: Implications for Membrane Anchoring and Base Pairing. J Phys Chem B 2004; 108:6485-97. [DOI: 10.1021/jp031188m] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Gosse
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - A. Boutorine
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - I. Aujard
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - M. Chami
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - A. Kononov
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - E. Cogné-Laage
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - J.-F. Allemand
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - J. Li
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
| | - L. Jullien
- Laboratoire de Physique Statistique CNRS UMR 8550, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Département de Chimie CNRS UMR 8640, Ecole Normale Supérieure, 24 rue Lhomond, F-75231 Paris Cedex 05, France, Laboratoire de Biophysique CNRS/MNHN UMR 5153, Muséum National d'Histoire Naturelle, 43 rue Cuvier, F-75231 Paris Cedex 05, France, and Laboratoire de Physico-Chimie CNRS UMR 168, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
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Boutorine AS, Ryabinin VA, Novopashina DS, Venyaminova AG, Hélène C, Sinyakov AS. Stabilization of DNA double and triple helices by conjugation of minor groove binders to oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1267-72. [PMID: 14565396 DOI: 10.1081/ncn-120022943] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
New conjugates containing two parallel or antiparallel carboxamide minor groove binders (MGB) attached to the same terminal phosphate of one oligonucleotide strand were synthesized. The conjugates interact with their target DNA stronger than the individual components. Effect of conjugated MGB on DNA duplex and triplex stability and their sequence specificity was demonstrated on the short oligonucleotide duplexes and on the triplex formed by model 16-mer oligonucleotide with HIV polypurine tract.
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Affiliation(s)
- A S Boutorine
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U 565, CNRS UMR 8646, Paris Cedex, France.
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Arimondo PB, Angenault S, Halby L, Boutorine A, Schmidt F, Monneret C, Garestier T, Sun JS, Bailly C, Hélène C. Spatial organization of topoisomerase I-mediated DNA cleavage induced by camptothecin-oligonucleotide conjugates. Nucleic Acids Res 2003; 31:4031-40. [PMID: 12853620 PMCID: PMC165972 DOI: 10.1093/nar/gkg457] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analysis of the DNA cleavage efficiency as a function of the positioning of the camptothecin derivative, either on the 3' or the 5' side of the triplex, and the location of the cleavage site. A previously identified cleavage site was inserted at different positions within two triplex site-containing 59 bp duplexes. Sequence-specific DNA cleavage by topoisomerase I occurs only with triplex conjugates bearing the inhibitor at the 3'-end of the oligonucleotide and on the oligopyrimidine strand of the duplex. The lack of targeted cleavage on the 5' side is attributed to the structural differences of the 3' and 5' duplex-triplex DNA junctions. The changes induced in the double helix by the triple-helical structure interfere with the action of the enzyme according to a preferred spatial organization. Camptothecin conjugates of oligonucleotides provide efficient tools to probe the organization of the topoisomerase I-DNA complex and will be useful to understand the functioning of topoisomerase I in living cells.
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Affiliation(s)
- Paola B Arimondo
- Laboratoire de Biophysique, USM0503 Muséum National d'Histoire Naturelle, UMR8646 CNRS, UR565 INSERM, 43 Rue Cuvier, 75231 Paris Cedex 05, France.
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Raddatz S, Mueller-Ibeler J, Kluge J, Wäss L, Burdinski G, Havens JR, Onofrey TJ, Wang D, Schweitzer M. Hydrazide oligonucleotides: new chemical modification for chip array attachment and conjugation. Nucleic Acids Res 2002; 30:4793-802. [PMID: 12409470 PMCID: PMC135808 DOI: 10.1093/nar/gkf594] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the synthesis of new phosphoramidite building blocks and their use for the modification of oligonucleotides with hydrazides. The reaction of these hydrazide oligonucleotides with active esters and aldehydes is demonstrated for solution conjugation and immobilization. Compared with the established amino modified oligonucleotides, hydrazides show enhanced reactivity at neutral and acidic buffer conditions. One method to introduce hydrazides is using amidites with preformed, protected hydrazides. A completely novel approach is the generation of the hydrazide functionality during the oligonucleotide cleavage and deprotection with hydrazine. Therefore, building blocks for the introduction of esters as hydrazide precursors are described. For the enhanced attachment on surfaces branched modifier amidites, which introduce up to four reactive groups to the oligonucleotide, are applied. The efficiency of branched hydrazide oligonucleotides compared with standard amino modified oligonucleotides for the immobilization of DNA on active electronic Nanogen chips is demonstrated.
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Affiliation(s)
- Stefan Raddatz
- Nanogen Recognomics GmbH, Industriepark Höchst G830, 65926 Frankfurt am Main, Germany and. Nanogen Inc., 10398 Pacific Center Court, San Diego, CA 92121, USA
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Grimm GN, Boutorine AS, Lincoln P, Nordén B, Hélène C. Formation of DNA triple helices by an oligonucleotide conjugated to a fluorescent ruthenium complex. Chembiochem 2002; 3:324-31. [PMID: 11933233 DOI: 10.1002/1439-7633(20020402)3:4<324::aid-cbic324>3.0.co;2-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A conjugate of a triple helix forming oligonucleotide (TFO) and the Lambda and Delta enantiomers of the ruthenium diphenanthroline dipyridophenazine complex [Ru(phen)(2)dppz](2+) was synthesized. The ruthenium complex was attached to the 5'-end of the TFO through the dppz moiety. This conjugate formed a stable triple helix with the polypurine tract (PPT) sequence from HIV proviral DNA. The thermal denaturation temperature of the triplex was increased by 12 degrees C. One remarkable property of the Delta-[Ru(phen)(2)dppz](2+) complex is a strong increase in its fluorescence when it intercalates into DNA. While the fluorescence of the oligonucleotide conjugate was very weak, the formation of a duplex with a complementary sequence or of a triple helix with a target duplex resulted in a large increase in fluorescence of the Delta enantiomer. The increase in fluorescence allowed us to follow the kinetics of duplex and triplex formation by fluorescence spectrometry. In contrast, the Lambda enantiomer gave a much smaller fluorescence change when a triplex was formed, even though the stability of the triplex was comparable to that of the Delta enantiomer. The property was ascribed to intercalation of the dipyridophenazine moiety of the Delta enantiomer into DNA and subsequent threading of the ruthenium complex through the DNA double helix. Salt effects were consistent with the involvement of DNA breathing in the formation of the intercalating complex.
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Affiliation(s)
- Günther N Grimm
- Laboratoire de Biophysique, INSERM 201-CNRS UMR 8646, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris Cedex 05, France
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Arimondo PB, Boutorine A, Baldeyrou B, Bailly C, Kuwahara M, Hecht SM, Sun JS, Garestier T, Hélène C. Design and optimization of camptothecin conjugates of triple helix-forming oligonucleotides for sequence-specific DNA cleavage by topoisomerase I. J Biol Chem 2002; 277:3132-40. [PMID: 11724801 DOI: 10.1074/jbc.m110181200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To achieve a sequence-specific DNA cleavage by topoisomerase I, derivatives of the antitumor drug camptothecin have been covalently linked to triple helix-forming oligonucleotides that bind in a sequence-specific manner to the major groove of double-helical DNA. Triplex formation at the target sequence positions the drug selectively at the triplex site, thereby stimulating topoisomerase I-mediated DNA cleavage at this site. In a continuous effort to optimize this strategy, a broad set of conjugates consisting of (i) 16-20-base-long oligonucleotides, (ii) alkyl linkers of variable length, and (iii) camptothecin derivatives substituted on the A or B quinoline ring were designed and synthesized. Analysis of the cleavage sites at nucleotide resolution reveals that the specificity and efficacy of cleavage depends markedly on the length of both the triple-helical structure and the linker between the oligonucleotide and the poison. The optimized hybrid molecules induced strong and highly specific cleavage at a site adjacent to the triplex. Furthermore, the drug-stabilized DNA-topoisomerase I cleavage complexes were shown to be more resistant to salt-induced reversal than the complexes induced by camptothecin alone. Such rationally designed camptothecin conjugates could provide useful antitumor drugs directed selectively against genes bearing the targeted triplex binding site. In addition, they represent a powerful tool to probe the molecular interactions in the DNA-topoisomerase I complex.
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Affiliation(s)
- Paola B Arimondo
- Laboratoire de Biophysique, UMR 8646 CNRS, Muséum National d'Histoire Naturelle, INSERM U201, 43 rue Cuvier, 75231 Paris cedex 05, France.
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Ros T, Bergamin M, Vázquez E, Spalluto G, Baiti B, Moro S, Boutorine A, Prato M. Synthesis and Molecular Modeling Studies of Fullerene−5,6,7-Trimethoxyindole−Oligonucleotide Conjugates as Possible Probes for Study of Photochemical Reactions in DNA Triple Helices. European J Org Chem 2002. [DOI: 10.1002/1099-0690(20022)2002:3<405::aid-ejoc405>3.0.co;2-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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