Influences of Linker and Nucleoside for the Helical Self-Assembly of Perylene Along DNA Templates

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.

Control of Energy Transfer Between Pyrene‐ and Perylene‐Nucleosides by the Sequence of DNA‐Templated Supramolecular Assemblies

“…We used DNA as template for the arrangement of chromophore‐nucleoside building blocks into multichromophoric systems with interesting optoelectronic properties, which were applied for light harvesting and could be processed in organic electronic devices . With respect to the building blocks it is important that chromophore and nucleoside are linked in a coplanar orientation, e. g. by the ethynylene linker . Hence, the sequence of chromophores and the chirality of such assemblies should be completely programmable by the DNA template.…”

“…The syntheses of Py‐dAp and Pe‐dU were previously reported. The preparation of the supramolecular chromophore DNA assemblies takes advantage of the high solubility of the chromophore‐nucleoside conjugates in organic solvents, in particular DMSO, and the low solubility in water.…”

Aggregation-induced emission by sequence-selective assembly of cyanolated distyrylbenzene in supramolecular DNA architectures

“…1(E)), like all our previous chromophore-ethynylene-dU conjugates. 7–9,19 Notably, the AIE with T 20 shows nearly the same maximum at 544 nm as the AIE with A 20 at 546 nm and differs from the emission of pure Cs-dU in water with a maximum at 558 nm, indicating the effect of hydrogen-bonding to the templates, mismatched with T 20 and matched with A 20 . Notably, Cs-dU is a modified T and provides hydrogen-bonding to another Cs-dU , but the AIE is small compared to the templated assemblies.…”

“…The ethynylene linker between the chromophore and 2 0 -deoxuridine is important because it allows coplanar orientation of the aromatic systems on both sides, which is a prerequisite for the successful DNAtemplated assembly. 19 Cs-dU shows a strong solvatochromic fluorescence (Fig. 1(B) and (C), Table S1 and Fig.…”

“…The chromophore sequence in these assemblies is encoded in the sequence of the DNA template, based on the canonical pairing of Cs-dU preferably to A 20 (see above) and Pe-dAp selectively to T 20 . 10,19 The mixed chromophore assemblies were prepared with A 10 T 10 and (AATT) 5 as DNA templates. Both templates have an identical number of binding sites for both Cs-dU and Pe-dAp, but different sequences, and identical length to the DNA templates A 20 and T 20 .…”