Robert Häner

Dialkynylpyrenes: Strongly Fluorescent, Environment-Sensitive DNA Building Blocks

Two isomeric dialkynylpyrene phosphoramidites and their incorporation into oligonucleotides are described. The pyrene units closely resemble the well-known perylene bisimide dye PDI with regard to the ability to self-organize within a DNA duplex. In addition, dialkynylpyrenes exhibit significant monomer and remarkably strong excimer fluorescence. The dialkynylpyrene building blocks are promising candidates for applications in diagnostic tools, such as excimer-based molecular beacons, as well as for novel DNA-based materials with special optical properties.

Formation of Two‐Dimensional Supramolecular Polymers by Amphiphilic Pyrene Oligomers

Reading the bands: Amphiphilic pyrene trimers self-assemble into two-dimensional, supramolecular polymers in aqueous medium. Folding and aggregation processes are accompanied by simultaneous development of J- and H-bands and significant changes in the fluorescence properties. The formation of sheet-like nano-structures is confirmed by AFM.

Highly efficient quenching of excimer fluorescence by perylene diimide in DNA.

Pyrene excimer fluorescence is effectively quenched by non-nucleosidic perylene diimides upon DNA duplex formation.

DNA‐Assisted Self‐Assembly of Pyrene Foldamers

The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating aromatic and phosphate groups ensures water solubility which, in turn, favors folding of the aromatic units. Pyrene molecules also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.

Control of aggregation-induced emission by DNA hybridization

Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Molecular aggregation and fluorescence of DATPEs are controlled by duplex formation.

Formation of Two Homo‐chromophoric H‐Aggregates in DNA‐Assembled Alternating Dye Stacks

The understanding and description of collectively excited multichromophores is of crucial importance for many areas of basic and applied research. DNA has been used for the construction of well-defined heterochromophoric stacks. Electronic coupling among non-adjacent chromophores of the same type leads to the co-existence of PDI and pyrene H-aggregates in hybrids composed of alternating chromophore stacks.

Signal control by self-assembly of fluorophores in a molecular beacon—a model study

Pyrene excimer fluorescence is efficiently regulated through formation of π-stacked aggregates between dialkynylpyrene (Y) and perylenediimide (E) residues located in the stem region of a molecular beacon (MB). The building blocks form organized, multichromophoric complexes in the native form. Hybridization to the target results in a conformational reorganization of the chromophores. The nature of the aggregates was investigated by changing the number of chromophores and natural base pairs in the beacon stem. The formation of different types of complexes (EYEY→YEY→EY) is revealed by characteristic spectroscopic changes. The data show that signal control is an intrinsic property of the interacting chromophores. The directed assembly of non-nucleosidic chromophores can be used for the generation of an on/off switch of a fluorescence signal. The concept may find applications in various types of light-based input/output systems.

A molecular probe for the detection of homopurine sequences.

Among the many types of oligonucleotide probes that are used in chemistry, biology, and the medical sciences for the detection and quantitation of nucleic acids, molecular beacons take a prominent role. Typically, a molecular beacon consists of a hairpin oligonucleotide with a fluorescent label and a quencher molecule at either end. In the absence of the target, the stem structure holds the dye molecules in close proximity, inhibiting fluorescence as a result of resonance energy transfer. 6] Upon hybridization of the beacon to its target, the stem melts, and the fluorophore and the quencher molecule are separated leading to the signal. In such molecular probe types, fluorescence is suppressed in the absence of the target ACHTUNGTRENNUNGsequence because of the proximity of the fluorescing and quenching molecules. Alternatively, a distinct diagnostic signal might also be generated by the proximity of two fluorophores, as for example, through the formation of an excimer. Efficient excimer or exciplex formation can be observed with pyrenes. Various types of oligonucleotide probes utilizing pyrene for this purpose have been described in the recent past. A special type of molecular beacon was reported which makes use of pyrene based excimer-to-monomer switching to differentiate between the absence of and the presence of a target. The highly specific detection of oligopurine strands is possible through formation of triple helical structures. In particular, synthetic oligonucleotides have been shown to adopt clamp-type motifs in which a homopurine strand is recognized by a homopyrimidine oligonucleotide through simultaneous formation of Watson–Crick and Hoog ACHTUNGTRENNUNGsteen bonds. As they recognize the target sequence by formation of two types of base-pairs at the same time, oligonucleotide clamps (also called “foldback” triplex-forming oligonucleotides) are particularly sensitive to mismatches. Furthermore, various synthetic modifications of clamp type oligonucleotides have been investigated with the aim of enhancing the binding affinity and/or specificity to homopurine target sequences. Fluorescence resonance energy transfer and excimer formation have been used for the investigation of the thermodynamic and kinetic rules of triplex formation. A triplex-forming molecular probe leading to the generation of an excimer would be a highly specific tool for the recognition of homopurine target sequences. The corresponding design would comprise a clamp-type homopyrimidine oligonucleotide with pyrene molecules attached to both ends, as illustrated in Scheme 1. The high mismatch susceptibility of the

Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly

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).

Triazolylpyrenes: Synthesis, fluorescence properties, and incorporation into DNA

Synthesis of 1,6- and 1,8-triazolylpyrenes and their incorporation into oligonucleotides is described. In hybrids, triazolylpyrenes adopt interstrand stacking interactions. Exciton coupling is observed for the duplex containing a pair of the 1,6-isomer indicating a well-defined helical arrangement of the triazolylpyrene building blocks. Triazole substitution results in pronounced red-shifts of monomer as well as excimer fluorescence. Furthermore, quantum yields of the formed excimers are remarkably high.