1
|
Sharma A, More SH, Ganesh KN. Electrostatics Favor PNA : DNA Stability over Stereochemistry in Pyrrolidine‐Based Cationic Dual‐Backbone PNA Analogues. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ashwani Sharma
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
- Department of Biology Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
| | - Shahaji H. More
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
| | - Krishna N. Ganesh
- Department of Chemistry Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
| |
Collapse
|
2
|
Konrad W, Fengler C, Putwa S, Barner‐Kowollik C. Schutzgruppenfreie Synthese von sequenzdefinierten Makromolekülen mittels präziser λ‐orthogonaler Photochemie. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Waldemar Konrad
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
| | - Christian Fengler
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
| | - Sarrah Putwa
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - Christopher Barner‐Kowollik
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
| |
Collapse
|
3
|
Konrad W, Fengler C, Putwa S, Barner-Kowollik C. Protection-Group-Free Synthesis of Sequence-Defined Macromolecules via Precision λ-Orthogonal Photochemistry. Angew Chem Int Ed Engl 2019; 58:7133-7137. [PMID: 30888105 DOI: 10.1002/anie.201901933] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Indexed: 01/10/2023]
Abstract
An advanced light-induced avenue to monodisperse sequence-defined linear macromolecules via a unique photochemical protocol is presented that does not require any protection-group chemistry. Starting from a symmetrical core unit, precision macromolecules with molecular weights up to 6257.10 g mol-1 are obtained via a two-monomer system: a monomer unit carrying a pyrene functionalized visible light responsive tetrazole and a photo-caged UV responsive diene, enabling an iterative approach for chain growth; and a monomer unit equipped with a carboxylic acid and a fumarate. Both light-induced chain growth reactions are carried out in a λ-orthogonal fashion, exciting the respective photosensitive group selectively and thus avoiding protecting chemistry. Characterization of each sequence-defined chain (size-exclusion chromatography (SEC), high-resolution electrospray ionization mass spectrometry (ESI-MS), and NMR spectroscopy), confirms the precision nature of the macromolecules.
Collapse
Affiliation(s)
- Waldemar Konrad
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131, Karlsruhe, Germany.,School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, QLD, 4000, Brisbane, Australia
| | - Christian Fengler
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131, Karlsruhe, Germany.,School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, QLD, 4000, Brisbane, Australia
| | - Sarrah Putwa
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131, Karlsruhe, Germany
| | - Christopher Barner-Kowollik
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131, Karlsruhe, Germany.,School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, QLD, 4000, Brisbane, Australia
| |
Collapse
|
4
|
Wang H, Feng Z, Qin Y, Wang J, Xu B. Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018; 57:4931-4935. [PMID: 29451962 PMCID: PMC6014697 DOI: 10.1002/anie.201712834] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/01/2018] [Indexed: 12/20/2022]
Abstract
Herein, we report that assemblies of nucleopeptides selectively sequester ATP in complex conditions (for example, serum and cytosol). We developed assemblies of nucleopeptides that selectively sequester ATP over ADP. Counteracting enzymes interconvert ATP and ADP to modulate the nanostructures formed by the nucleopeptides and the nucleotides. The nucleopeptides, sequestering ATP effectively in cells, slow down efflux pumps in multidrug-resistant cancer cells, thus boosting the efficacy of doxorubicin, an anticancer drug. Investigation of 11 nucleopeptides (including d- and l-enantiomers) yields five more nucleopeptides that differentiate ATP and ADP through either precipitation or gelation. As the first example of assemblies of nucleopeptides that interact with ATP and disrupt intracellular ATP dynamics, this work illustrates the use of supramolecular assemblies to interact with small and essential biological molecules for controlling cell behavior.
Collapse
Affiliation(s)
- Huaimin Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Zhaoqianqi Feng
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Yanan Qin
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Jiaqing Wang
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| | - Bing Xu
- Department of chemistry, Brandeis University, 415 South St, Waltham, MA, 02454, USA
| |
Collapse
|
5
|
Nucleopeptide Assemblies Selectively Sequester ATP in Cancer Cells to Increase the Efficacy of Doxorubicin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712834] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
6
|
Konrad W, Bloesser FR, Wetzel KS, Boukis AC, Meier MAR, Barner‐Kowollik C. A Combined Photochemical and Multicomponent Reaction Approach to Precision Oligomers. Chemistry 2018; 24:3413-3419. [DOI: 10.1002/chem.201705939] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Waldemar Konrad
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
- Institut für Biologische Grenzflächen Karlsruhe Institute of, Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street, QLD 4000 Brisbane Australia
| | - Fabian R. Bloesser
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
- Institut für Biologische Grenzflächen Karlsruhe Institute of, Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street, QLD 4000 Brisbane Australia
- Laboratory of Applied Chemistry, Institut für Organische Chemie Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Katharina S. Wetzel
- Laboratory of Applied Chemistry, Institut für Organische Chemie Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Andreas C. Boukis
- Laboratory of Applied Chemistry, Institut für Organische Chemie Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Michael A. R. Meier
- Laboratory of Applied Chemistry, Institut für Organische Chemie Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Christopher Barner‐Kowollik
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
- Institut für Biologische Grenzflächen Karlsruhe Institute of, Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street, QLD 4000 Brisbane Australia
| |
Collapse
|
7
|
Ovadia R, Mondielli C, Vasseur JJ, Baraguey C, Alvarez K. Contribution to PNA-RNA Chimera Synthesis: One-Pot Microwave-Assisted Ugi Reaction to Obtain Dimeric Building Blocks. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Reuben Ovadia
- Laboratoire d'Architecture et Fonction des Macromolécules Biologiquesm; Université Aix-Marseille UMR CNRS 7257; Equipe “Antiviral Medicinal Chemistry”; Parc scientifique de Luminy, 163 av. de Luminy 13288 Marseille Cedex 9 France
| | - Clémence Mondielli
- Laboratoire d'Architecture et Fonction des Macromolécules Biologiquesm; Université Aix-Marseille UMR CNRS 7257; Equipe “Antiviral Medicinal Chemistry”; Parc scientifique de Luminy, 163 av. de Luminy 13288 Marseille Cedex 9 France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS - Université Montpellier-ENSCM; Département des Analogues et Constituants des Acides Nucléiques, Equipe “ Oligonucléotides Modifiés ”; Bâtiment 17, Campus Triolet, Place Eugène Bataillon 34095 Montpellier Cedex 5 France
| | - Carine Baraguey
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247 CNRS - Université Montpellier-ENSCM; Département des Analogues et Constituants des Acides Nucléiques, Equipe “ Oligonucléotides Modifiés ”; Bâtiment 17, Campus Triolet, Place Eugène Bataillon 34095 Montpellier Cedex 5 France
| | - Karine Alvarez
- Laboratoire d'Architecture et Fonction des Macromolécules Biologiquesm; Université Aix-Marseille UMR CNRS 7257; Equipe “Antiviral Medicinal Chemistry”; Parc scientifique de Luminy, 163 av. de Luminy 13288 Marseille Cedex 9 France
| |
Collapse
|
8
|
Pathigoolla A, Sureshan KM. Synthesis of Triazole-linked Homonucleoside Polymers through Topochemical Azide-Alkyne Cycloaddition. Angew Chem Int Ed Engl 2014; 53:9522-5. [DOI: 10.1002/anie.201404797] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 12/24/2022]
|
9
|
Pathigoolla A, Sureshan KM. Synthesis of Triazole-linked Homonucleoside Polymers through Topochemical Azide-Alkyne Cycloaddition. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404797] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
10
|
Hüsken N, Gębala M, La Mantia F, Schuhmann W, Metzler-Nolte N. Mechanistic studies of Fc-PNA(⋅DNA) surface dynamics based on the kinetics of electron-transfer processes. Chemistry 2011; 17:9678-90. [PMID: 21735492 DOI: 10.1002/chem.201003764] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/31/2011] [Indexed: 12/28/2022]
Abstract
N-Terminally ferrocenylated and C-terminally gold-surface-grafted peptide nucleic acid (PNA) strands were exploited as unique tools for the electrochemical investigation of the strand dynamics of short PNA(⋅DNA) duplexes. On the basis of the quantitative analysis of the kinetics and the diffusional characteristics of the electron-transfer process, a nanoscopic view of the Fc-PNA(⋅DNA) surface dynamics was obtained. Loosely packed, surface-confined Fc-PNA single strands were found to render the charge-transfer process of the tethered Fc moiety diffusion-limited, whereas surfaces modified with Fc-PNA⋅DNA duplexes exhibited a charge-transfer process with characteristics between the two extremes of diffusion and surface limitation. The interplay between the inherent strand elasticity and effects exerted by the electric field are supposed to dictate the probability of a sufficient approach of the Fc head group to the electrode surface, as reflected in the measured values of the electron-transfer rate constant, k(0). An in-depth understanding of the dynamics of surface-bound PNA and PNA⋅DNA strands is of utmost importance for the development of DNA biosensors using (Fc-)PNA recognition layers.
Collapse
Affiliation(s)
- Nina Hüsken
- Inorganic Chemistry I, Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | | | | | | | | |
Collapse
|
11
|
Svensen N, Díaz-Mochón JJ, Dhaliwal K, Planonth S, Dewar M, Armstrong JD, Bradley M. Screening of a Combinatorial Homing Peptide Library for Selective Cellular Delivery. Angew Chem Int Ed Engl 2011; 50:6133-6. [DOI: 10.1002/anie.201101804] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
12
|
Svensen N, Díaz-Mochón JJ, Dhaliwal K, Planonth S, Dewar M, Armstrong JD, Bradley M. Screening of a Combinatorial Homing Peptide Library for Selective Cellular Delivery. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101804] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
13
|
Hüsken N, Gebala M, Schuhmann W, Metzler-Nolte N. A single-electrode, dual-potential ferrocene-PNA biosensor for the detection of DNA. Chembiochem 2010; 11:1754-61. [PMID: 20602405 DOI: 10.1002/cbic.200900748] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A Fc-PNA biosensor (Fc: ferrocenyl, C(10)H(9)Fe) was designed by using two electrochemically distinguishable recognition elements with different molecular information at a single electrode. Two Fc-PNA capture probes were therefore synthesized by N-terminal labeling different dodecamer PNA sequences with different ferrocene derivatives by click chemistry. Each of the two strands was thereby tethered with one specific ferrocene derivative. The two capture probes revealed quasi-reversible redox processes of the Fc(0/+) redox couple with a significant difference in their electrochemical half-wave potentials of Delta E(1/2)=160 mV. A carefully designed biosensor interface, consisting of a ternary self-assembled monolayer (SAM) of the two C-terminal cysteine-tethered Fc-PNA capture probes and 6-mercaptohexanol, was electrochemically investigated by square wave (SWV) and cyclic voltammetry (CV). The biosensor properties of this interface were analyzed by studying the interaction with DNA sequences that were complementary to either of the two capture probes by SWV. Based on distinct changes in both peak current and potential, a parallel identification of these two DNA sequences was successful with one interface design. Moreover, the primary electrochemical response could be converted by a simple mathematical analysis into a clear-cut electrochemical signal about the hybridization event. The discrimination of single-nucleotide polymorphism (SNP) was proven with a chosen single-mismatch DNA sequence. Furthermore, experiments with crude bacterial RNA confirm the principal suitability of this dual-potential sensor under real-life conditions.
Collapse
Affiliation(s)
- Nina Hüsken
- Lehrstuhl für Anorganische Chemie I, Bioanorganische Chemie, Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
| | | | | | | |
Collapse
|
14
|
Kwak M, Herrmann A. Nucleic Acid/Organic Polymer Hybrid Materials: Synthesis, Superstructures, and Applications. Angew Chem Int Ed Engl 2010; 49:8574-87. [DOI: 10.1002/anie.200906820] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
15
|
Kwak M, Herrmann A. Hybridmaterialien aus Nucleinsäuren und organischen Polymeren: Synthese, Überstrukturen und Anwendungen. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906820] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
16
|
Grossmann TN, Seitz O. Nucleic acid templated reactions: consequences of probe reactivity and readout strategy for amplified signaling and sequence selectivity. Chemistry 2009; 15:6723-30. [PMID: 19496097 DOI: 10.1002/chem.200900025] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA- and RNA-templated chemical reactions can serve as a diagnostic means for the detection of nucleic acids. Reaction schemes that allow amplified detection are of high interest for polymerase chain reaction (PCR)-free DNA and RNA diagnosis. These reactions typically draw upon the catalytic activity of the template, which is able to trigger the conversion of many signaling molecules per template molecule. However, the design of reactive probes that allow both sensitive and selective nucleic acid detection is a challenge and requires insight into three major parameters: a) reactivity of functional groups involved, b) affinity of probes for the template, and c) the readout system. In this study we used peptide nucleic acid (PNA)-based probes to investigate in detail the signaling power and the selectivity of a transfer reaction derived from a native chemical ligation. We show that subtle variations of the thioesters involved had a tremendous impact on the sensitivity and selectivity of the reaction system. The results suggest that reactions at turnover conditions require low rates of non-templated reaction pathways to provide high target selectivity and sensitivity. On the other hand, very high rates of templated reactions should be avoided to allow mismatched probe-template complexes to dissociate prior to bond formation. Furthermore, the temperature dependence of the DNA-catalyzed transfer reaction was studied and provided insight into crucial strand-exchange processes. Further improvements of selective signaling were achieved through a new readout based on pyrene-transfer reactions. This method reduces background signals and enables significant increases in the signaling rates compared with previous fluorescence-based methods.
Collapse
Affiliation(s)
- Tom N Grossmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | | |
Collapse
|
17
|
Boussalah N, Touzani R, Bouabdallah I, Kadiri SE, Ghalem S. Synthesis, structure and catalytic properties of tripodal amino-acid derivatized pyrazole-based ligands. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcata.2009.02.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
18
|
Pfeifer S, Lutz JF. Development of a Library ofN-Substituted Maleimides for the Local Functionalization of Linear Polymer Chains. Chemistry 2008; 14:10949-57. [DOI: 10.1002/chem.200801237] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
19
|
Synthesis of 3-(4-Amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)propanoic acid – A Functionalized Base Derivative of the Nucleoside Antibiotic Tubercidin. MOLBANK 2007. [DOI: 10.3390/m555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
20
|
Baldoli C, Rigamonti C, Maiorana S, Licandro E, Falciola L, Mussini PR. A new triferrocenyl-tris(hydroxymethyl)aminomethane derivative as a highly sensitive electrochemical marker of biomolecules: application to the labelling of PNA monomers and their electrochemical characterization. Chemistry 2007; 12:4091-100. [PMID: 16544344 DOI: 10.1002/chem.200501466] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have designed and synthesised a new organometallic molecule containing three ferrocene groups for use as a highly sensitive electrochemical marker in biological assays. This trisferrocene derivative was conjugated to different PNA monomers, and the electrochemical activities of the conjugates were extensively investigated in organic solvents, in view of their potential diagnostic applications. The results showed that the introduction of a trisferrocene unit on the PNA monomer triples the current signal in comparison with the monoferrocene-labelled one. Despite their greater molecular complexity, trisferrocene-conjugated PNA monomers are even more electrochemically active than the reference ferrocene. By using differential pulse voltammetry (DPV), the detection limit can reach 10(-8) M in acetonitrile solution. These results are a good premise for the use of the trisferrocene unit as an effective electrochemical probe for biomolecules.
Collapse
Affiliation(s)
- Clara Baldoli
- CNR-Institute of Molecular Science and Technologies, Via C. Golgi 19, 20133 Milano, Italy
| | | | | | | | | | | |
Collapse
|
21
|
Englund EA, Appella DH. Gamma-substituted peptide nucleic acids constructed from L-lysine are a versatile scaffold for multifunctional display. Angew Chem Int Ed Engl 2007; 46:1414-8. [PMID: 17133633 DOI: 10.1002/anie.200603483] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
22
|
Englund E, Appella D. γ-Substituted Peptide Nucleic Acids Constructed fromL-Lysine are a Versatile Scaffold for Multifunctional Display. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603483] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
23
|
Harris JL, Winssinger N. PNA encoding (PNA=peptide nucleic acid): from solution-based libraries to organized microarrays. Chemistry 2006; 11:6792-801. [PMID: 16038006 DOI: 10.1002/chem.200500305] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Microarray-based technologies have attracted attention in chemical biology by virtue of their miniaturized format, which is well suited to probe ligand-protein interactions or investigate enzymatic activity in complex biological mixtures. A number of research groups have reported the preparation of surfaces on microarrays with specific functional groups to chemoselectively attach small molecules from libraries. We have developed an alternative method whereby libraries are encoded with peptide nucleic acid (PNA), such that libraries which exist as mixtures in solution self-assemble into an organized microarray through hybridization to produce readily available DNA arrays. This allows libraries synthesized by split and mix methods to be decoded in a single step. An asset of this method compared to direct spotting is that libraries can be used in solution for bioassays prior to self-assembly into the microarray format.
Collapse
Affiliation(s)
- Jennifer L Harris
- Department of Chemistry, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | | |
Collapse
|
24
|
Affiliation(s)
- Dave R van Staveren
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | | |
Collapse
|
25
|
Hamzavi R, Happ T, Weitershaus K, Metzler-Nolte N. The use of 3,3-bis(2-imidazolyl) propionic acid (bip-OH) as a new chelating ligand for Re(CO)3 and Ru complexes: Formation of organometallic PNA oligomers with (bip)Re(CO)3 and their interaction with complementary DNA. J Organomet Chem 2004. [DOI: 10.1016/j.jorganchem.2004.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
26
|
Affiliation(s)
- Alexander Heckel
- Universität Bonn, Kekulé-Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
| |
Collapse
|
27
|
Seitz O, Köhler O. Convergent strategies for the attachment of fluorescing reporter groups to peptide nucleic acids in solution and on solid phase. Chemistry 2001; 7:3911-25. [PMID: 11596933 DOI: 10.1002/1521-3765(20010917)7:18<3911::aid-chem3911>3.0.co;2-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The site-selective conjugation of peptide nucleic acids (PNA) with fluorescent reporter groups is essential for the construction of hybridisation probes that can report the presence of a particular DNA sequence. This paper describes convergent methods for the solution- and solid-phase synthesis of multiply labelled PNA oligomers. The solid-phase synthesis of protected PNA enabled the selective attachment of fluorescent labels at the C-terminal end (3' in DNA) which demonstrated that further manipulations on protected PNA fragments are feasible. For the conjugation to internal sites, a method is introduced that allows for the on-resin assembly of modified monomers thereby omitting the need to synthesise an entire monomer in solution. Furthermore, it is shown that the application of a highly orthogonal protecting group strategy in combination with chemoselective conjugation reactions provides access to a rapid and automatable solid-phase synthesis of dual labelled PNA probes. Real-time measurements of nucleic acid hybridisation were possible by taking advantage of the fluorescence resonance energy transfer (FRET) between suitably appended fluorophoric groups. Analogously to DNA-based molecular beacons, the dual labelled PNA probes were only weakly fluorescing in the single-stranded state. Hybridisation to a complementary oligonucleotide, however, induced a structural reorganisation and conferred a vivid fluorescence enhancement.
Collapse
Affiliation(s)
- O Seitz
- Department of Chemical Biology and Institut für Organische Chemie, Universität Dortmund, Germany.
| | | |
Collapse
|
28
|
Mattes A, Seitz O. Multiplex-Nachweis von Einzelbasenpolymorphie in DNA durch massenspektrometrische Verfolgung einer PNA-Verknüpfung. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010903)113:17<3277::aid-ange3277>3.0.co;2-o] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
29
|
Mattes A, Seitz O. Mass-Spectrometric Monitoring of a PNA-Based Ligation Reaction for the Multiplex Detection of DNA Single-Nucleotide Polymorphisms. Angew Chem Int Ed Engl 2001; 40:3178-3181. [DOI: 10.1002/1521-3773(20010903)40:17<3178::aid-anie3178>3.0.co;2-m] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2001] [Revised: 06/05/2001] [Indexed: 12/11/2022]
|
30
|
Demidov VV, Broude NE, Lavrentieva-Smolina IV, Kuhn H, Frank-Kamenetskii MD. An artificial primosome: design, function, and applications. Chembiochem 2001; 2:133-9. [PMID: 11828437 DOI: 10.1002/1439-7633(20010202)2:2<133::aid-cbic133>3.0.co;2-l] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Double-stranded (ds) DNA is capable of the sequence-specific accommodation of an additional oligodeoxyribonucleotide strand by the peptide nucleic acid(PNA)-assisted formation of a so-called PD-loop. We demonstrate here that the PD-loop may function as an artificial primosome within linear, nonsupercoiled DNA duplexes. DNA polymerase with its strand displacement activity uses this construct to initiate the primer extension reaction at a designated dsDNA site. The primer is extended by several hundred nucleotides. The efficiency of dsDNA priming by the artificial primosome assembly is comparable to the single-stranded DNA priming used in various assays. The ability of the PD-loop structure to perform like an artificial primosome on linear dsDNA may find applications in biochemistry, molecular biology, and molecular biotechnology, as well as for DNA diagnostics. In particular, multiple labels can be incorporated into a chosen dsDNA site resulting in ultrasensitive direct quantification of specific sequences. Furthermore, nondenaturing dsDNA sequencing proceeds from the PD-loop. This approach opens the way to direct isothermal reading of the DNA sequence against a background of unrelated DNA, thereby eliminating the need for purification of the target DNA.
Collapse
Affiliation(s)
- V V Demidov
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
| | | | | | | | | |
Collapse
|
31
|
Seitz O. Festphasensynthese doppelt markierter Peptidnucleinsäuren als Sonden für die Echtzeitdetektion der Hybridisierung. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/1521-3757(20000915)112:18<3389::aid-ange3389>3.0.co;2-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
32
|
Seitz O. Solid-Phase Synthesis of Doubly Labeled Peptide Nucleic Acids as Probes for the Real-Time Detection of Hybridization This work was supported by the Fonds der Chemischen Industrie. Angew Chem Int Ed Engl 2000; 39:3249-3252. [PMID: 11028066 DOI: 10.1002/1521-3773(20000915)39:18<3249::aid-anie3249>3.0.co;2-m] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- O Seitz
- Max-Planck-Institut für Molekulare Physiologie Abteilung Chemische Biologie Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
| |
Collapse
|
33
|
Schütz R, Cantin M, Roberts C, Greiner B, Uhlmann E, Leumann C. Olefinische Peptidnucleinsäuren (OPAs): neue Aspekte hinsichtlich der Erkennung von DNA durch PNA. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/(sici)1521-3757(20000403)112:7<1305::aid-ange1305>3.0.co;2-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
34
|
Seitz O. Chemisch modifizierte Antisense-Oligonucleotide: neue Fortschritte auf dem Gebiet der Bindung von RNA und der Aktivierung der Ribonuclease H. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19991203)111:23<3674::aid-ange3674>3.0.co;2-n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
35
|
Seitz O, Bergmann F, Heindl D. Eine konvergente Strategie zur Modifizierung von Peptidnucleinsäuren: neue PNA-Hybridisierungssonden zum Nachweis von Basen-Fehlpaarungen. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990802)111:15<2340::aid-ange2340>3.0.co;2-n] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
36
|
Kuhn H, Demidov VV, Frank-Kamenetskii MD. Topologische Verbindung zwischen einer Doppelstrang-DNA und einer ringförmigen Einzelstrang-DNA. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19990517)111:10<1544::aid-ange1544>3.0.co;2-o] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|