A DNA mimic made of non-nucleosidic phenanthrene building blocks

Sequence-complementarity dependent co-assembly of phosphodiester-linked aromatic donor–acceptor trimers

Sequence-defined trimers of phosphodiester-linked aromatic donor–acceptors self-assemble according to monomer order, and co-assemble into new structures with their complementary sequence.

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).

Modulation of chiroptical properties by DNA-guided assembly of fluorenes

The supramolecular organization of fluorene building blocks in a DNA scaffold is described. The molecular assembly into ordered π-aggregates leads to distinct changes in the electronic properties.

Photophysical characterization of oligopyrene modules for DNA-based nanosystems

The photophysics of free pyrenedicarboxamide (Py-DCA) in solution as well as of single-stranded and double-stranded oligonucleotides (ss and ds ONs) containing 1-7 pyrene building blocks per strand were studied by steady-state and time-resolved fluorescence spectroscopy. It was found that the fluorescence quantum yield Phi(F) of free Py-DCA chromophore in solution is rather high (Phi(F) = 0.44). However, after incorporation of the chromophore into a ss ON the monomeric chromophore fluorescence is quenched more than 40-fold due to electron-transfer reactions with ON bases. An increase of the number n of neighboring pyrenes in an ON results in Phi(F) growth up to 0.25 at n = 6. Starting from n = 2, all fluorescence belongs mainly to excimer formed by pyrene chromophores. Sections composed of multiple pyrenes may be considered as robust functional entities that may serve as independent modules in DNA-based, functional nano-architectures.

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.

DNA as a supramolecular framework for the helical arrangements of chromophores: towards photoactive DNA-based nanomaterials

Nucleic acids have been emerging as supramolecular structural scaffolds for the helical organization of chromophores in the creation of functional nanomaterials mainly because of the their unique structural features and synthetic accessibility. A large number of chromophores have been successfully incorporated into DNA or RNA as C-nucleosides, as base surrogates or as modified sugars using solid phase phosphoramidite chemistry. Moreover, multiple incorporations yield the helical organization of the chromophores inside or outside the DNA or RNA double helix depending upon the conjugation of the chromophores. Significant photophysical interactions are observed in the chromophore stacks resulting in unique optical properties that are significantly different from the monomer properties. In this feature article, multichromophore labelled nucleic acids are reviewed with special emphasis on the self-assembly induced modulation of the optical properties.

DNA containing non-nucleosidic phenanthrene building blocks with asymmetrical linkers

The synthesis and hybridization properties of oligonucleotides containing phenanthrene building blocks with non-nucleosidic linkers of different length are described. It was found that the length of the linkers, as well as the combination of unequal linkers can have a substantial influence on the thermal stability of the modified DNA.

Spectroscopic properties of pyrene-containing DNA mimics

DNA mimics containing non-nucleosidic pyrene building blocks are described. The modified oligomers form stable hybrids, although a slight reduction in hybrid stability is observed in comparison to the unmodified DNA duplex. The nature of the interaction between the pyrene residues in single and double stranded oligomers is analyzed spectroscopically. Intra- and interstrand stacking interactions of pyrenes are monitored by UV-absorbance as well as fluorescence spectroscopy. Excimer formation is observed in both single and double strands. In general, intrastrand excimers show fluorescence emission at shorter wavelengths (approx. 5-10 nm) than excimers formed by interstrand interactions. The existence of two different forms of excimers (intra- vs. interstrand) is also revealed in temperature dependent UV-absorbance spectra.

Fluorescent DNA base modifications and substitutes: multiple fluorophore labeling and the DETEQ concept

There is an increasing need for fluorescent nucleic acid probes that are able to sense genetic variations without the application of enzymes. The incorporation of organic fluorophores either as DNA base modifications or as DNA base substitutions represents a powerful and versatile method for such new fluorescent DNA assays. Multiple labeling of oligonucleotides using several adjacent chromophore-modified DNA bases yields fluorescence enhancement and modulation that are sensitive to single-base mismatches in the complementary oligonucleotide. Charge transfer processes that cause fluorescence quenching are DNA-base mediated and occur over several base pairs distance. Our "DETEQ" setup, consisting of a fluorescence DNA base substitution and the charge acceptor as a second modification two base pairs away, allows the homogeneous detection of single-base mutations simply by fluorescence readout. This could lead to new DNA microarrays which are based on charge transfer processes and can be analyzed by commonly used fluorescence readout techniques.

The genetic incorporation of a distance probe into proteins in Escherichia coli

The unnatural amino acid p-nitrophenylalanine (pNO2-Phe) was genetically introduced into proteins in Escherichia coli in response to the amber nonsense codon with high fidelity and efficiency by means of an evolved tRNA/aminoacyl-tRNA synthetase pair from Methanocuccus jannaschii. It was shown that pNO2-Phe efficiently quenches the intrinsic fluorescence of Trp in a distance-dependent manner in a model GCN4 basic region leucine zipper (bZIP) protein. Thus, the pNO2-Phe/Trp pair should be a useful biophysical probe of protein structure and function.

Selectivity in DNA interstrand-stacking

The synthesis and spectroscopic investigation of DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks is reported. It was found that interstrand-stacking of the polyaromatic compounds in the DNA duplex takes place with a high degree of selectivity.