Exciplex fluorescence emission from simple organic intramolecular constructs in non-polar and highly polar media as model systems for DNA-assembled exciplex detectors

c-kit2 G-quadruplex stabilized via a covalent probe: exploring G-quartet asymmetry

Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (U^py) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with U^py and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.

The endeavor of vibration-induced emission (VIE) for dynamic emissions

Organic chromophores with large Stokes shifts and dual emissions are fascinating because of their fundamental and applied interest. Vibration-induced emission (VIE) refers to a tunable multiple fluorescence exhibited by saddle-shaped N,N'-disubstituted-dihydribenzo[a,c]phenazines (DHPs), which involves photo-induced configuration vibrations from bent to planar form along the N-N axis. VIE-active molecules show intrinsic long-wavelength emissions in the unconstrained state (planar state) but bright short-wavelength emissions in the constrained state (bent state). The emission response for VIE-active luminogens is highly sensitive to steric hindrance encountered during the planarization process such that a tiny structural variation can induce an evident change in fluorescence. This can often be achieved by tuning the intensity ratio of short- and long-wavelength bands. In some special cases, the alterations in the emission wavelength of VIE fluorophores can be achieved step by step by harnessing the degree of bending angle motion in the excited state. In this perspective, we summarize the latest progress in the field of VIE research. New bent heterocyclic structures, as novel types of VIE molecules, are being developed, and the general features of the chemical structures are also being proposed. Technologically, novel emission color-tuning approaches and VIE-based probes for visualizing biological activity are presented to demonstrate how the dynamic VIE effect can be exploited for cutting-edge applications.

Anion identification using silsesquioxane cages

Anthracene-conjugated octameric silsesquioxane cages thermodynamically display intramolecular excimer formation, which can be used to identify anions through the change of fluorescence.

Anthracene-conjugated octameric silsesquioxane (AnSQ) cages, prepared via Heck coupling between octavinylsilsesquioxane (OVS) and 9-bromoanthracene, thermodynamically display intramolecular excimer emissions. More importantly, these hosts are sensitive to each anionic guest, thereby resulting in change of anthracene excimer formation, displaying the solvent-dependent fluorescence and allowing us to distinguish up to four ions such as F^–, OH^–, CN^– and PO₄^3– by fluorescence spectroscopy. Depending on the solvent polarity, for example, both F^– and CN^– quenched the fluorescence emission intensity in THF, but only F^– could enhance the fluorescence in all other solvents. The presence of PO₄^3– results in fluorescence enhancements in high polarity solvents such as DMSO, DMF, and acetone, while OH^– induces enhancements only in low polarity solvents (e.g. DCM and toluene). A picture of the anion recognizing ability of AnSQ was obtained through principal component analysis (PCA) with NMR and FTIR confirming the presence of host–guest interactions. Computational modeling studies demonstrate the conformation of host–guest complexation and also the change of excimer formation. Detection of F^–, CN^– and OH^– by AnSQ hosts in THF is noticeable with the naked eye, as indicated by strong color changes arising from charge transfer complex formation upon anion addition.

Self-reversible mechanochromism and aggregation induced emission in neutral triarylmethanes and their application in water sensing

Neutral triarylmethanes exhibit intramolecular exciplex formation, self-reversible mechanochromism, and aggregation induced/viscosity-dependent emission and sense water in organic solvents.

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

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.

Molecular probes: insights into design and analysis from computational and physical chemistry

The application of new molecular diagnostics to probe cellular process in vivo is leading to a greater understanding of molecular cytology at a sub-nanoscale level and is opening the way to individualized medicines. We review here three distinct fluorescence-based molecular probes, HyBeacons, split-probe exciplexes and GFP (green fluorescent protein)-based FRET (fluorescence resonance energy transfer) systems. Through this, we highlight the insights into the mechanism and design that a combined computational and experimental approach can yield.

Target-assembled exciplexes based on Scorpion oligonucleotides

Scorpion probes, specific DNA probe sequences maintained in a hairpin–loop, can be modified to carry the components of an exciplex for use as a novel fluorescence-based method for specific detection of DNA. The exciplex partners (5′-pyrenyl and 3′-naphthalenyl) were attached to oligonucleotides via phosphoramidate links to terminal phosphate groups. Hybridization of the probe to a complementary target in a buffer containing trifluoroethanol produced an obvious fluorescence change from blue (pyrene locally excited state emission) to green (exciplex emission).

Artificial DNAs based on alkynyl C-nucleosides as a superior scaffold for homo- and heteroexcimer emissions

DNA-like fluorescent oligomers composed of alkynyl beta-D-ribofuranosides bearing pyrene, perylene, and anthracene as a fluorophore were synthesized by solid-phase DNA synthesis. The fluorescent oligomers possess the defined number and order of the fluorophores. In these oligomers, the adjacent fluorophores efficiently interact with each other by hydrophobic interactions in their electronic ground states in a face-to-face fashion. The predominant excimer emissions were observed from not only the homooligomers (pyrene-pyrene and perylene-perylene systems) but also the heterooligomers (pyrene-perylene, pyrene-anthracene, and perylene-anthracene systems) in aqueous media.

Detection of nucleic acids in situ: novel oligonucleotide analogues for target-assembled DNA-mounted exciplexes

This research describes the effects of structural variation and medium effects for the novel split-oligonucleotide (tandem) probe systems for exciplex-based fluorescence detection of DNA. In this approach the detection system is split at a molecular level into signal-silent components, which must be assembled correctly into a specific 3-dimensional structure to ensure close proximity of the exciplex partners and the consequent exciplex fluorescence emission on excitation. The model system consists of two 8-mer oligonucleotides, complementary to adjacent sites of a 16-mer DNA target. Each probe oligonucleotide is equipped with functions able to form an exciplex on correct, contiguous hybridization. This study investigates the influence of a number of structural aspects (i.e. chemical structure and composition of exciplex partners, length and structure of linker groups, locations of exciplex partner attachment, as well as effects of media) on the performance of DNA-mounted exciplex systems. The extremely rigorous structural demands for exciplex formation and emission required careful structural design of linkers and partners for exciplex formation, which are here described. Certain organic solvents (especially trifluoroethanol) specifically favour emission of the DNA-mounted exciplexes, probably the net result of the particular duplex structure and specific solvation of the exciplex partners. The exciplexes formed emitted at approximately 480 nm with large Stokes shifts ( approximately 130-140 nm). Comparative studies with pyrene excimer systems were also carried out.

Conformational analysis of r207910, a new drug candidate for the treatment of tuberculosis, by a combined NMR and molecular modeling approach

R207910 is an enantiomeric compound from a new class of antimycobacterial agents, the diarylquinolines [Science; 307:223 (2005)]. As enantiospecific interaction is required for biologic activity, we have undertaken a combined nuclear magnetic resonance and molecular modeling study to gain new insights into its conformation in solution and its absolute configuration. A conformational analysis using a Monte-Carlo method has been performed on each of the four possible stereomers of this compound leading to the identification of their most stable conformation. Additional ab initio calculation was performed with emphasis on the strength of the observed intramolecular hydrogen bond. Simultaneously, a complete structural identification has been carried out by a set of monodimensional and bidimensional (1)H-(13)C-NMR experiments. Determination of inter-proton distances has been achieved by a series of (1)H-(1)H ROESY NMR experiments with different mixing times followed by a volume quantification of the correlations peaks. These experimental data were compared with the theoretical distances obtained from the conformational analysis. The remarkable match shows that R207910 adopts one of the low-energy conformations predicted by molecular modeling and belongs to the (RS, SR) couple of diastereoisomers. A posteriori validation of our approach has been performed by X-ray structure determination that concluded for the RS configuration.