Simon Matthias Langenegger

Excimer formation by interstrand stacked pyrenes

Non-nucleosidic, pyrene-derived base surrogates form excimers via interstrand stacking in duplex DNA.

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.

The Effect of a Non-nucleosidic Phenanthrene Building Block on DNA Duplex Stability

Oligonucleotides containing a phenanthrene-derived, non-nucleosidic building block with flexible linkers were synthesized. The effect of the phenanthrene moiety on duplex stability at different positions was investigated. Placement of two phenanthrene residues in opposite positions had a slightly positive effect on duplex stability. This positive effect was further increased, when two phenanthrene pairs were juxtaposed. In contrast, introduction of a single phenanthrene unit opposite to an adenosine or a thymidine led to a destabilization of the duplex. A model of a phenanthrene-modified duplex is proposed.

Remarkable stabilization of duplex DNA containing an abasic site by non-nucleosidic phenanthroline and pyrene building blocks.

Abasic sites represent a common type of lesion in DNA. Loss of a base can take place as a spontaneous process, it can happen as a result of base modification, or it can occur during an enzymatic repair process. 3] If not repaired, the resulting abasic site has a high potential for mutagenicity or might lead to cell death. Due to their biological importance, there is a strong interest in methods of recognizing abasic sites in DNA both for diagnostic and pharmaceutical use. Intercalating ligands have been evaluated as inhibitors of enzymatic repair processes to increase the efficacy of cytotoxic agents. Stabilization of abasic sites in duplex DNA has been achieved with complementary oligonucleotides carrying extended aromatic residues opposite to the abasic site. Thus, deoxyribofuranosides carrying pyrene and other polyaromatic hydrocarbons have been used as substitutes for missing nucleobases in order to maintain the aromatic stacking throughout the duplex. We have recently reported that phenanthrene substituted with flexible aliphatic linkers can be used to stabilize abasic sites in a DNA duplex. Such building blocks might present a considerable practical advantage over the synthetically more demanding sugar-derived analogues. From a structural point of view, an abasic site represents a discontinuity of

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.

Long‐Distance Electronic Energy Transfer in Light‐Harvesting Supramolecular Polymers

The efficient collection of solar energy relies on the design and construction of well-organized light-harvesting systems. Herein we report that supramolecular phenanthrene polymers doped with pyrene are effective collectors of light energy. The linear polymers are formed through the assembly of short amphiphilic oligomers in water. Absorption of light by phenanthrene residues is followed by electronic energy transfer along the polymer over long distances (>100 nm) to the accepting pyrene molecules. The high efficiency of the energy transfer, which is documented by large fluorescence quantum yields, suggests a quantum coherent process.

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

Light-Harvesting Nanotubes Formed by Supramolecular Assembly of Aromatic Oligophosphates

A 2,7-disubstituted phosphodiester-linked phenanthrene trimer forms tubular structures in aqueous media. Chromophores are arranged in H-aggregates. Incorporation of small quantities of pyrene results in the development of light-harvesting nanotubes in which phenanthrenes act as antenna chromophores and pyrenes as energy acceptors. Energy collection is most efficient after excitation at the phenanthrene H-band. Fluorescence quantum yields up to 23 % are reached in pyrene doped, supramolecular nanotubes.

Assembling Multiporphyrin Stacks Inside the DNA Double Helix

Double stranded DNA hybrids containing up to four consecutive, face-to-face stacked porphyrins are described. Non-nucleosidic, 5,15-bisphenyl-substituted porphyrin building blocks were incorporated into complementary oligonucleotide strands. Upon hybridization multiple porphyrins are well accommodated inside the DNA scaffold without disturbing the overall B-DNA structure. The formation of double strands containing up to four free base porphyrins is enabled without compromising duplex stability. UV/vis, fluorescence, and CD spectroscopy demonstrate the formation of porphyrins H-aggregates inside the DNA double helix and provide evidence for the existence of strong excitonic coupling between interstrand stacked porphyrins. H-aggregation results in considerable fluorescence quenching. Most intense CD effects are observed in stacks containing four porphyrins. The findings demonstrate the value of DNA for the controlled formation of molecularly defined porphyrin aggregates.