Programmable and Sequence‐Selective Supramolecular Assembly of Two Different Chromophores along DNA Templates

Abstract

The templated self-assembly of two different chromophores attached to the same binding motif gives oligomers of statistical mixtures without any control on the resulting chromophore sequence. The first self-assembled bichromophore system is reported, in which the resulting chromophore sequence is simply governed by the DNA template. A new ethynylpyrene-diaminopurine 2'-deoxynucleoside was combined with the ethynyl nile red-modified 2'-deoxyuridine to achieve this completely programmable sequence selective self-assembly. The helical ordering of the two different chromophores by DNA templates with different mixtures of A-T sequences yields precise control over the optical properties of the formed assemblies, which was proven by methods of optical spectroscopy.

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

“…The fluorescence intensities by the energy transfer between the chromophores increase in the mixed assemblies along the DNA templates from A 10 T 10 over (AATT) 5 to (AT) 10 , although these three templates provide equal numbers of potential binding sites for the two different nucleoside chromophore conjugates and exhibit similar absorbances. This stands in contrast to our previous studies with Py‐dAp and a nile red‐dU conjugate where the sequence controls fluorescence quenching by energy transfer between the two chromophores . We previously showed that nearly every binding site of single‐stranded DNA templates are occupied by chromophore‐nucleoside conjugates .…”

“…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.…”

From Interaction to Function in DNA‐Templated Supramolecular Self‐Assemblies

“…Notable developments of this approach are expected by harnessing the power of DNA‐templating to program a well‐defined sequence of multiple chromophores based on the DNA mother sequence. A significant step in this direction has been recently reported by Wagenknecht et al ., who synthesized a pyrene derivative bound to an A‐type nucleoside, and another compound made of a nile red derivative bound to U‐type nucleoside (Figure ) . The former pairs to a thymine base, while the latter pairs to an adenine base.…”

“…They mixed these two chromophores with various types of DNA templates made of either pure T, pure A, and mixed A−T sequences. In the mixed sequences, optical spectroscopy clearly indicates the formation of arrays based on a sequence‐selective assembly of the two chromophores along the DNA template . Furthermore, the same group reported the design of identical chromophores (ethynylpyrene and nile red derivatives), each attached to the same uracil base, but with either to d ‐ or l ‐sugars (2’‐deoxyribofuranosides).…”