51
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Griffith JA, Withers JM, Martin DJ, Rowlands GJ, Filichev VV. Ligand assembly and chirality transfer guided by DNA modified with enantiomerically pure [2.2]paracyclophanes. RSC Adv 2013. [DOI: 10.1039/c3ra41841c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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52
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Biner SM, Häner R. DNA Triplex-Mediated Assembly of Polyaromatic Chromophores. Chem Biodivers 2012; 9:2485-93. [DOI: 10.1002/cbdv.201200276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Indexed: 12/22/2022]
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53
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Avirah RR, Schuster GB. Fluorescence Quenching by Intercalation of a Pyrene Group Tethered to anN4-modified Cytosine in Duplex DNA. Photochem Photobiol 2012; 89:332-5. [DOI: 10.1111/j.1751-1097.2012.01243.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 09/11/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Rekha R. Avirah
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta; GA; USA
| | - Gary B. Schuster
- School of Chemistry and Biochemistry; Georgia Institute of Technology; Atlanta; GA; USA
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54
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Yang W, Chen Y, Wong MS, Lo PK. Reinforced Self-Assembly of Donor–Acceptor π-Conjugated Molecules to DNA Templates by Dipole–Dipole Interactions Together with Complementary Hydrogen Bonding Interactions for Biomimetics. Biomacromolecules 2012; 13:3370-6. [DOI: 10.1021/bm301131k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wanggui Yang
- Department of Chemistry and Institute of Molecular Functional Materials, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR
| | - Yali Chen
- Department of Chemistry, Shanghai University, Shanghai, China
| | - Man Shing Wong
- Department of Chemistry and Institute of Molecular Functional Materials, Hong Kong Baptist University, Kowloon Tong, Hong Kong,
SAR
| | - Pik Kwan Lo
- Department of Biology
and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR
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55
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Sezi S, Varghese R, Vilaivan T, Wagenknecht HA. Conformational Control of Dual Emission by Pyrrolidinyl PNA-DNA Hybrids. ChemistryOpen 2012; 1:173-6. [PMID: 24551507 PMCID: PMC3922446 DOI: 10.1002/open.201200016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Indexed: 01/09/2023] Open
Affiliation(s)
- Sabrina Sezi
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
| | - Reji Varghese
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University Phyathai Road, Pathumwan, Bangkok 10330 (Thailand) E-mail:
| | - Hans-Achim Wagenknecht
- Institute for Organic Chemistry, Karlsruhe Institute of Technology Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany) E-mail:
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56
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Barrois S, Wagenknecht HA. Diarylethene-modified nucleotides for switching optical properties in DNA. Beilstein J Org Chem 2012; 8:905-14. [PMID: 23015841 PMCID: PMC3388881 DOI: 10.3762/bjoc.8.103] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 05/09/2012] [Indexed: 01/03/2023] Open
Abstract
Diarylethenes were attached to the 5-position of 2’-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures.
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Affiliation(s)
- Sebastian Barrois
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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57
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Nussbaumer AL, Samain F, Malinovskii VL, Häner R. Supramolecular polymerization of oligopyrenotides--control by single, natural nucleotides. Org Biomol Chem 2012; 10:4891-8. [PMID: 22610059 DOI: 10.1039/c2ob25320h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Amphiphilic heptapyrenotides (Py(7)) assemble into supramolecular polymers. Here we present a comprehensive spectroscopic study of aggregates and co-aggregates of the non-chiral Py(7) and its mono- or di-substituted nucleotide analogs (Py(7)-N and N-Py(7)-N'). The data show that the formation of supramolecular polymers from oligopyrenotides is highly sensitive to the nature of the attached, chiral auxiliary. A single natural nucleotide may be sufficient for the fine tuning of the aggregates' properties by changing the mechanism of aggregation from an isodesmic to a nucleation-elongation process, which results in a high degree of amplification of chirality in the formed supramolecular polymers. Watson-Crick complementarity does not play a significant role, since co-aggregates of oligomers modified with complementary nucleotides show no signs of supramolecular polymerization. Depending on the nucleotide, the helical sense of the polymers is shifted to an M-helix or a P-helix. The findings demonstrate the value of oligopyrenotides as oligomeric building blocks for the generation of optically active supramolecular polymers.
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Affiliation(s)
- Alina L Nussbaumer
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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58
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Tanaka M, Oguma K, Saito Y, Saito I. Enhancement of fluorescence quenching and exciplex formation in DNA major groove by double incorporation of modified fluorescent deoxyuridines. Bioorg Med Chem Lett 2012; 22:4103-5. [PMID: 22578464 DOI: 10.1016/j.bmcl.2012.04.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/07/2012] [Accepted: 04/13/2012] [Indexed: 12/30/2022]
Abstract
5-(1-Naphthalenylethynyl)-2'-deoxyuridine ((N)U) and 5-[(4-cyano-1-naphthalenyl)ethynyl]-2'-deoxyuridine ((CN)U) were synthesized and incorporated into oligodeoxynucleotides. Fluorescence emissions of modified duplexes containing double (N)U were efficiently quenched depending upon the sequence pattern of the naphthalenes in DNA major groove, as compared to the duplex possessing single (N)U. When one of the naphthalene moieties has a cyano substituent, the exciplex emission from the chromophores in DNA major groove was observed at longer wavelength.
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Affiliation(s)
- Makiko Tanaka
- Department of Chemical Biology and Applied Chemistry, School of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
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59
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: chiral nanoscale templates for chromophore assembly. Angew Chem Int Ed Engl 2012; 51:4905-8. [PMID: 22492542 DOI: 10.1002/anie.201201352] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Indexed: 01/29/2023]
Abstract
Getting organized: DNA-like supramolecular polymers formed of short oligopyrenotides serve as a helical scaffold for the molecular assembly of ligands. The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT).
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60
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201352] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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61
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Polymethine dyes as spectral-fluorescent probes for biomacromolecules. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2011.11.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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62
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Zhao JS, Wang JH, He WB, Ruan YB, Jiang YB. Isolable chiral aggregates of achiral π-conjugated carboxylic acids. Chemistry 2012; 18:3631-6. [PMID: 22328175 DOI: 10.1002/chem.201103651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Indexed: 11/11/2022]
Abstract
The induced aggregation of achiral building blocks by a chiral species to form chiral aggregates with memorized chirality has been observed for a number of systems. However, chiral memory in isolated aggregates of achiral building blocks remains rare. One possible reason for this discrepancy could be that not much is understood in terms of designing these chiral aggregates. Herein, we report a strategy for creating such isolable chiral aggregates from achiral building blocks that retain chiral memory after the facile physical removal of the chiral templates. This strategy was used for the isolation of chiral homoaggregates of neutral achiral π-conjugated carboxylic acids in pure aqueous solution. Under what we have termed an "interaction-substitution" mechanism, we generated chiral homoaggregates of a variety of π-conjugated carboxylic acids by using carboxymethyl cellulose (CMC) as a mediator in acidic aqueous solutions. These aggregates were subsequently isolated from the CMC templates whilst retaining their memorized supramolecular chirality. Circular dichroism (CD) spectra of the aggregates formed in the acidic CMC solution exhibited bisignated exciton-coupled signals of various signs and intensities that were maintained in the isolated pure homoaggregates of the achiral π-conjugated carboxylic acids. The memory of the supramolecular chirality in the isolated aggregates was ascribed to the substitution of COOH/COOH hydrogen-bonding interaction between the carboxylic acid groups within the aggregates for the hydrogen-bonding interactions between the COOH groups of the building blocks and the chiral templates. We expect that this "interaction-substitution" procedure will open up a new route to isolable pure chiral aggregates from achiral species.
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Affiliation(s)
- Jin-Song Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering and the MOE Key Laboratory of Analytical Sciences, Xiamen University, Xiamen 361005, PR China
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63
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Probst M, Wenger D, Biner SM, Häner R. The DNA three-way junction as a mould for tripartite chromophore assembly. Org Biomol Chem 2012; 10:755-9. [DOI: 10.1039/c1ob06400b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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64
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Burns JR, Preus S, Singleton DG, Stulz E. A DNA based five-state switch with programmed reversibility. Chem Commun (Camb) 2012; 48:11088-90. [DOI: 10.1039/c2cc35799b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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65
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Lin J, Surin M, Beljonne D, Lou X, van Dongen JLJ, Schenning APHJ. On the mechanism of dynamic polymerization via recycled ss-DNA templated assembly of non-natural bases. Chem Sci 2012. [DOI: 10.1039/c2sc20389h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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66
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Chen W, Schuster GB. DNA-Programmed Modular Assembly of Cyclic and Linear Nanoarrays for the Synthesis of Two-Dimensional Conducting Polymers. J Am Chem Soc 2011; 134:840-3. [DOI: 10.1021/ja210007f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Wen Chen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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68
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Garo F, Häner R. A DNA-based light-harvesting antenna. Angew Chem Int Ed Engl 2011; 51:916-9. [PMID: 22162263 DOI: 10.1002/anie.201103295] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/18/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Florian Garo
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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69
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Tanaka M, Kozakai R, Saito Y, Saito I. Stabilization of DNA duplex by 2-substituted adenine as a minor groove modifier. Bioorg Med Chem Lett 2011; 21:7021-4. [DOI: 10.1016/j.bmcl.2011.09.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/24/2011] [Accepted: 09/27/2011] [Indexed: 01/07/2023]
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70
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Guo Z, De Cat I, Van Averbeke B, Lin J, Wang G, Xu H, Lazzaroni R, Beljonne D, Meijer EW, Schenning APHJ, De Feyter S. Nucleoside-Assisted Self-Assembly of Oligo(p-phenylenevinylene)s at Liquid/Solid Interface: Chirality and Nanostructures. J Am Chem Soc 2011; 133:17764-71. [DOI: 10.1021/ja206437c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zongxia Guo
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Inge De Cat
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Bernard Van Averbeke
- Service de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Jianbin Lin
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Guojie Wang
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Hong Xu
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Roberto Lazzaroni
- Service de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - David Beljonne
- Service de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - E. W. Meijer
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Albertus P. H. J. Schenning
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Steven De Feyter
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
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71
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Petkau K, Kaeser A, Fischer I, Brunsveld L, Schenning APHJ. Pre- and postfunctionalized self-assembled π-conjugated fluorescent organic nanoparticles for dual targeting. J Am Chem Soc 2011; 133:17063-71. [PMID: 21913650 DOI: 10.1021/ja2075345] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
There is currently a high demand for novel approaches to engineer fluorescent nanoparticles with precise surface properties suitable for various applications, including imaging and sensing. To this end, we report a facile and highly reproducible one-step method for generating functionalized fluorescent organic nanoparticles via self-assembly of prefunctionalized π-conjugated oligomers. The engineered design of the nonionic amphiphilic oligomers enables the introduction of different ligands at the extremities of inert ethylene glycol side chains without interfering with the self-assembly process. The intrinsic fluorescence of the nanoparticles permits the measurement of their surface properties and binding to dye-labeled target molecules via Förster resonance energy transfer (FRET). Co-assembly of differently functionalized oligomers is also demonstrated, which enables the tuning of ligand composition and density. Furthermore, nanoparticle prefunctionalization has been combined with subsequent postmodification of azide-bearing oligomers via click chemistry. This allows for expanding ligand diversity at two independent stages in the nanoparticle fabrication process. The practicability of the different methods entails greater control over surface functionality. Through labeling with different ligands, selective binding of proteins, bacteria, and functionalized beads to the nanoparticles has been achieved. This, in combination with the absence of unspecific adsorption, clearly demonstrates the broad potential of these nanoparticles for selective targeting and sequestration. Therefore, controlled bifunctionalization of fluorescent π-conjugated oligomer nanoparticles represents a novel approach with high applicability to multitargeted imaging and sensing in biology and medicine.
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Affiliation(s)
- Katja Petkau
- Laboratory of Chemical Biology, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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