101
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Dallmann A, Beribisky AV, Gnerlich F, Rübbelke M, Schiesser S, Carell T, Sattler M. Site-Specific Isotope-Labeling of Inosine Phosphoramidites and NMR Analysis of an Inosine-Containing RNA Duplex. Chemistry 2016; 22:15350-15359. [DOI: 10.1002/chem.201602784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Indexed: 01/09/2023]
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102
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Su M, Kirchner A, Stazzoni S, Müller M, Wagner M, Schröder A, Carell T. 5-Formylcytosine Could Be a Semipermanent Base in Specific Genome Sites. Angew Chem Int Ed Engl 2016; 55:11797-800. [PMID: 27561097 DOI: 10.1002/anie.201605994] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 12/22/2022]
Abstract
5-Formyl-2'-deoxycytosine (fdC) is a recently discovered epigenetic base in the genome of stem cells, with yet unknown functions. Sequencing data show that the base is enriched in CpG islands of promoters and hence likely involved in the regulation of transcription during cellular differentiation. fdC is known to be recognized and excised by the enzyme thymine-DNA-glycosylase (Tdg). As such, fdC is believed to function as an intermediate during active demethylation. In order to understand the function of the new epigenetic base fdC, it is important to analyze its formation and removal at defined genomic sites. Here, we report a new method that combines sequence-specific chemical derivatization of fdC with droplet digital PCR that enables such analysis. We show initial data, indicating that the repair protein Tdg removes only 50 % of the fdCs at a given genomic site, arguing that fdC is a semipermanent base.
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103
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Su M, Kirchner A, Stazzoni S, Müller M, Wagner M, Schröder A, Carell T. 5-Formylcytosin ist vermutlich eine semipermanente Base an definierten Genompositionen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605994] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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104
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Schröder AS, Kotljarova O, Parsa E, Iwan K, Raddaoui N, Carell T. Synthesis of (R)-Configured 2′-Fluorinated mC, hmC, fC, and caC Phosphoramidites and Oligonucleotides. Org Lett 2016; 18:4368-71. [DOI: 10.1021/acs.orglett.6b02110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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105
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Greco CM, Kunderfranco P, Rubino M, Larcher V, Carullo P, Anselmo A, Kurz K, Carell T, Angius A, Latronico MVG, Papait R, Condorelli G. DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy. Nat Commun 2016; 7:12418. [PMID: 27489048 PMCID: PMC4976219 DOI: 10.1038/ncomms12418] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Abstract
Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC)-5-mC's oxidation product-in cardiac biology and disease is unknown. Here we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks during heart development and failure. DNA hydroxymethylation marks the body of highly expressed genes as well as distal regulatory regions with enhanced activity. Moreover, pathological hypertrophy is characterized by a shift towards a neonatal 5-hmC distribution pattern. We also show that the ten-eleven translocation 2 (TET2) enzyme regulates the expression of key cardiac genes, such as Myh7, through 5-hmC deposition on the gene body and at enhancers. Thus, we provide a genome-wide analysis of 5-hmC in the cardiomyocyte and suggest a role for this epigenetic modification in heart development and disease.
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106
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Becker S, Thoma I, Deutsch A, Gehrke T, Mayer P, Zipse H, Carell T. A high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway. Science 2016; 352:833-6. [PMID: 27174989 DOI: 10.1126/science.aad2808] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 03/15/2016] [Indexed: 11/03/2022]
Abstract
The origin of life is believed to have started with prebiotic molecules reacting along unidentified pathways to produce key molecules such as nucleosides. To date, a single prebiotic pathway to purine nucleosides had been proposed. It is considered to be inefficient due to missing regioselectivity and low yields. We report that the condensation of formamidopyrimidines (FaPys) with sugars provides the natural N-9 nucleosides with extreme regioselectivity and in good yields (60%). The FaPys are available from formic acid and aminopyrimidines, which are in turn available from prebiotic molecules that were also detected during the Rosetta comet mission. This nucleoside formation pathway can be fused to sugar-forming reactions to produce pentosides, providing a plausible scenario of how purine nucleosides may have formed under prebiotic conditions.
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107
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Datz S, Argyo C, Gattner M, Weiss V, Brunner K, Bretzler J, von Schirnding C, Torrano AA, Spada F, Vrabel M, Engelke H, Bräuchle C, Carell T, Bein T. Genetically designed biomolecular capping system for mesoporous silica nanoparticles enables receptor-mediated cell uptake and controlled drug release. NANOSCALE 2016; 8:8101-8110. [PMID: 27021414 DOI: 10.1039/c5nr08163g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Effective and controlled drug delivery systems with on-demand release and targeting abilities have received enormous attention for biomedical applications. Here, we describe a novel enzyme-based cap system for mesoporous silica nanoparticles (MSNs) that is directly combined with a targeting ligand via bio-orthogonal click chemistry. The capping system is based on the pH-responsive binding of an aryl-sulfonamide-functionalized MSN and the enzyme carbonic anhydrase (CA). An unnatural amino acid (UAA) containing a norbornene moiety was genetically incorporated into CA. This UAA allowed for the site-specific bio-orthogonal attachment of even very sensitive targeting ligands such as folic acid and anandamide. This leads to specific receptor-mediated cell and stem cell uptake. We demonstrate the successful delivery and release of the chemotherapeutic agent Actinomycin D to KB cells. This novel nanocarrier concept provides a promising platform for the development of precisely controllable and highly modular theranostic systems.
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108
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Carell T, Vrabel M. Erratum to: Bioorthogonal Chemistry—Introduction and Overview. Top Curr Chem (Cham) 2016; 374:12. [DOI: 10.1007/s41061-016-0014-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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109
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Carell T, Vrabel M, Yang M, Yang Y, Chen PR, Dommerholt J, Rutjes FPJT, van Delft FL, Herner A, Lin Q, Wu H, Devaraj NK, Kath-Schorr S. M. Vrabel and T. Carell for Cycloadditions in Bioorthogonal Chemistry. Top Curr Chem (Cham) 2016; 374:15. [DOI: 10.1007/s41061-016-0017-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/19/2016] [Indexed: 11/25/2022]
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110
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Klier L, Aranzamendi E, Ziegler D, Nickel J, Karaghiosoff K, Carell T, Knochel P. Lewis Acid Triggered Regioselective Magnesiation and Zincation of Uracils, Uridines, and Cytidines. Org Lett 2016; 18:1068-71. [DOI: 10.1021/acs.orglett.6b00190] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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111
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Bucher DB, Kufner CL, Schlueter A, Carell T, Zinth W. UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair. J Am Chem Soc 2015; 138:186-90. [PMID: 26651219 DOI: 10.1021/jacs.5b09753] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Absorption of UV-radiation in nucleotides initiates a number of photophysical and photochemical processes, which may finally cause DNA damage. One major decay channel of photoexcited DNA leads to reactive charge transfer states. This study shows that these states trigger self-repair of DNA photolesions. The experiments were performed by UV spectroscopy and HPLC on different single and double stranded oligonucleotides containing a cyclobutane pyrimidine dimer (CPD) lesion. In a first experiment we show that photoexcitation of adenine adjacent to a CPD has no influence on this lesion. However, excitation of a guanine (G) adenine (A) sequence leads to reformation of the intact thymine (T) bases. The involvement of two bases for the repair points to a long-living charge transfer state between G and A to be responsible for the repair. The negatively charged A radical anion donates an electron to the CPD, inducing ring splitting and repair. In contrast, a TA sequence, having an inverted charge distribution (T radical anion, A radical cation), is not able to repair the CPD lesion. The investigations show that the presence of an adjacent radical ion is not sufficient for repair. More likely it is the driving power represented by the oxidation potential of the radical ion, which controls the repair. Thus, repair capacities are strongly sequence-dependent, creating DNA regions with different tendencies of self-repair. This self-healing activity represents the simplest sequence-dependent DNA repair system.
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112
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Carell T. DNA-Reparatur. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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113
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Gassen NC, Fries GR, Zannas AS, Hartmann J, Zschocke J, Hafner K, Carrillo-Roa T, Steinbacher J, Preißinger SN, Hoeijmakers L, Knop M, Weber F, Kloiber S, Lucae S, Chrousos GP, Carell T, Ising M, Binder EB, Schmidt MV, Rüegg J, Rein T. Chaperoning epigenetics: FKBP51 decreases the activity of DNMT1 and mediates epigenetic effects of the antidepressant paroxetine. Sci Signal 2015; 8:ra119. [DOI: 10.1126/scisignal.aac7695] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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114
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Abstract
DNA is constantly damaged by various endogenous and exogenous events. Repair systems constantly scan the genome for DNA lesions and replace damaged and mismatched bases, which finally enables the complex DNA double strand to store genetic information. This year's Nobel Prize in Chemistry was awarded to pioneers in this field, T. Lindahl, P. Modrich, and A. Sancar.
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115
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Wagner M, Steinbacher J, Kraus TFJ, Michalakis S, Hackner B, Pfaffeneder T, Perera A, Müller M, Giese A, Kretzschmar HA, Carell T. Age-dependent levels of 5-methyl-, 5-hydroxymethyl-, and 5-formylcytosine in human and mouse brain tissues. Angew Chem Int Ed Engl 2015; 54:12511-4. [PMID: 26137924 PMCID: PMC4643189 DOI: 10.1002/anie.201502722] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/13/2015] [Indexed: 12/25/2022]
Abstract
The absolute levels of 5-hydroxymethylcytosine (hmC) and 5-methylcytosine (mC) in human brain tissues at various ages were determined. Additionally, absolute levels of 5-formylcytosine (fC) in adult individuals and cytosine modification levels in sorted neurons were quantified. These data were compared with age-related fC, hmC, and mC levels in mouse brain samples. For hmC, an initial steady increase is observed, which levels off with age to a final steady-state value of 1.2 % in human brain tissue. This level is nearly twice as high as in mouse cerebral cortex. In contrast, fC declines rapidly with age during early developmental stages, thus suggesting that while hmC is a stable epigenetic mark, fC is more likely an intermediate of active DNA demethylation during early brain development. The trends in global cytosine modification dynamics during the lifespan of an organism are conserved between humans and mice and show similar patterns in different organs.
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116
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Wagner M, Steinbacher J, Kraus TFJ, Michalakis S, Hackner B, Pfaffeneder T, Perera A, Müller M, Giese A, Kretzschmar HA, Carell T. Altersabhängige Level von 5-Methyl-, 5-Hydroxymethyl- und 5-Formylcytosin in Hirngeweben des Menschen und der Maus. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502722] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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117
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Bucher DB, Pilles BM, Carell T, Zinth W. Dewar Lesion Formation in Single- and Double-Stranded DNA is Quenched by Neighboring Bases. J Phys Chem B 2015; 119:8685-92. [DOI: 10.1021/acs.jpcb.5b04694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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118
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Benjdia A, Heil K, Winkler A, Carell T, Schlichting I. Rescuing DNA repair activity by rewiring the H-atom transfer pathway in the radical SAM enzyme, spore photoproduct lyase. Chem Commun (Camb) 2015; 50:14201-4. [PMID: 25285338 DOI: 10.1039/c4cc05158k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radical SAM enzyme, spore photoproduct lyase, requires an H-atom transfer (HAT) pathway to catalyze DNA repair. By rational engineering, we demonstrate that it is possible to rewire its HAT pathway, a first step toward the development of novel catalysts based on the radical SAM enzyme scaffold.
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119
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Schuster L, Rothmund L, He X, Van Landuyt KL, Schweikl H, Hellwig E, Carell T, Hickel R, Reichl FX, Högg C. Effect of Opalescence® bleaching gels on the elution of dental composite components. Dent Mater 2015; 31:745-57. [DOI: 10.1016/j.dental.2015.03.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/10/2015] [Accepted: 03/31/2015] [Indexed: 11/17/2022]
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120
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Rothmund L, Shehata M, Van Landuyt KL, Schweikl H, Carell T, Geurtsen W, Hellwig E, Hickel R, Reichl FX, Högg C. Release and protein binding of components from resin based composites in native saliva and other extraction media. Dent Mater 2015; 31:496-504. [DOI: 10.1016/j.dental.2015.01.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 01/24/2015] [Accepted: 01/28/2015] [Indexed: 01/06/2023]
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121
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Ehrlich M, Gattner MJ, Viverge B, Bretzler J, Eisen D, Stadlmeier M, Vrabel M, Carell T. Orchestrating the Biosynthesis of an Unnatural Pyrrolysine Amino Acid for Its Direct Incorporation into Proteins Inside Living Cells. Chemistry 2015; 21:7701-4. [DOI: 10.1002/chem.201500971] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 12/31/2022]
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122
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Benjdia A, Heil K, Winkler A, Carell T, Schlichting I. Structural Perspectives on the Mechanism of the Radical SAM Enzyme, Spore Photoproduct Lyase. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.895.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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123
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Schiesser S, Hackner B, Vrabel M, Beck W, Carell T. Synthesis and DNA-Damaging Properties of Cisplatin-N-Mustard Conjugates. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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124
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Penter L, Maier B, Frede U, Hackner B, Carell T, Hagemeier C, Truss M. A rapid screening system evaluates novel inhibitors of DNA methylation and suggests F-box proteins as potential therapeutic targets for high-risk neuroblastoma. Target Oncol 2015; 10:523-33. [DOI: 10.1007/s11523-014-0354-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 12/18/2014] [Indexed: 01/28/2023]
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125
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Su M, Tomás-Gamasa M, Carell T. DNA based multi-copper ions assembly using combined pyrazole and salen ligandosides. Chem Sci 2015; 6:632-638. [PMID: 28936312 PMCID: PMC5588782 DOI: 10.1039/c4sc01567c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/05/2014] [Indexed: 01/16/2023] Open
Abstract
The DNA structure is an ideal building block for the construction of functional nano-objects. In this direction, metal coordinating base pairs (ligandosides) are an appealing tool for the future specific functionalization of such nano-objects. We present here a study, in which we combine the metal ion coordinating pyrazole ligandoside with the interstrand crosslinking salen ligandoside system. We show that both ligandosides, when combined, are able to create stable multi-copper ion complexing DNA double helix structures in a cooperative fashion.
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