Abstract
Six different conjugates of perylene with 2′-deoxyuridine and with 2-amino-2′-deoxyadenosine were synthesized and applied for DNA-templated assembly in aqueous buffer solutions. They differ by the linkers ethynylene, phenylene, and phenylene–ethynylene between nucleoside and chromophore. The nucleosides were investigated as monomers in CHCl3 and dimethyl sulfoxide by optical spectroscopy. The properties of the four phenylene-linked conjugates are similar to that of perylene as reference because these linkers separate both aromatic parts. The ethynylene linker electronically couples the chromophore with the respective nucleoside and thus red shifts the absorbance. The DNA-templated assembly properties were elucidated by mixing the templates in aqueous buffer with the perylene–nucleoside conjugates from a dimethyl sulfoxide stock solution. Specific binding of the nucleosides was probed by comparing the results with dA20 and T20 as single-stranded DNA templates. Our studies reveal the structural parameters that are important for the DNA-templated assembly of perylenes. First, perylene-2′-deoxyuridine conjugates do not form DNA-templated helical assemblies, regardless of the choice of linker. Second, the ethynylene linker is crucial for successful DNA-templated chromophore assemblies of perylene-2-amino-2′-deoxyadenosine conjugates. Third, in contrast, the phenylene linker inhibits self-assembly along single-stranded DNA templates. In conclusion, the 2-amino-2′-deoxyadenosin in combination with the ethynylene linker provides the best structural feature for specific and helical DNA-templated assembly of perylenes. This result is important for the design of future DNA-based supramolecular architectures with chromophores, in particular DNA-based light-harvesting systems and DNA systems for emitting or sensing circularly polarized luminescence.
Highlights
Supramolecular chemistry and supramolecular polymerization summarize the efforts to self-organize molecules through interactions in a precise and controllable way
We study the self-assembly of these nucleoside conjugates and the influence of the corresponding single-stranded DNA templates oligothymidine (T20) and oligo-2′-deoxyadenosine in comparison by methods of optical spectroscopy to characterize their optical and chiroptical properties
The ethynylene group connects the perylene chromophore with the nucleosides in a coplanar orientation and thereby yields π-conjugation between them, whereas the phenylene group electronically isolates the π-systems by rotation
Summary
Supramolecular chemistry and supramolecular polymerization summarize the efforts to self-organize molecules through interactions in a precise and controllable way. The sequence-defined recognition by canonical base pairing in DNA in combination with a perfectly coplanar stacking distance of 3.4 Å and a helical chirality should yield supramolecular architectures (Burge et al, 2006). Such architectures are difficult to be achieved by simple organicchemical building blocks without DNA, neither covalently (polymers) nor non-covalently (supramolecular polymers). The controlled assembly of organic chromophores in supramolecular architectures based on nucleic acids holds the key potential for future functional materials with well-defined photochemical properties. The helical twist between the chromophores, which is induced by the DNA scaffold, controls electron transfer and energy transfer processes and thereby reduces the self-quenching that is typically observed in chromophore aggregates (Asanuma et al, 2003; Teo et al, 2009; Dutta et al, 2011; Kato et al, 2013; Li et al, 2013; Probst et al, 2014; Ishutkina et al, 2018)
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