Solvent induced changes in the electronic structure of a polar intermolecular exciplex

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

Organic intramolecular exciplexes, N-(4-dimethylaminobenzyl)-N-(1-pyrenemethyl)amine (1) and N'-4-dimethylaminonaphthyl-N-(1-pyrenemethyl)amine (2), were used as model systems to reveal major factors affecting their exciplex fluorescence, and thus lay the basis for developing emissive target-assembled exciplexes for DNA-mounted systems in solution. These models with an aromatic pyrenyl hydrocarbon moiety as an electron acceptor appropriately connected to an aromatic dimethylamino electron donor component (N,N-dimethylaminophenyl or N,N-dimethylaminonaphthyl) showed strong intramolecular exciplex emission in both non-polar and highly polar solvents. The effect of dielectric constant on the maximum wavelength for exciplex emission was studied, and emission was observed for 1 and 2 over the full range of solvent from non-polar hydrocarbons up to N-methylformamide with a dielectric constant of 182. Quantum yields were determined for these intramolecular exciplexes in a range of solvents relative to that for Hoechst 33,258. Conformational analysis of 1 was performed both computationally and via qualitative 2D NMR using (1)H-NOESY experiments. The results obtained indicated the contribution of pre-folded conformation(s) to the ground state of 1 conducive to exciplex emission. This research provides the initial background for design of self-assembled, DNA-mounted exciplexes and underpins further development of exciplex-based hybridisation bioassays.

The inter-relationship between triplet energies and spin chemistry

Triplet energies play a considerable role in optical spectroscopy, and can be determined from phosphorescence or the quenching thereof. Their role in spin chemistry may not be as obvious, but the triplet state has always had an important function or utility, namely of reaction intermediates such as radical pairs, their precursors, of carbenes, and of the final products. In situ NMR spectroscopy represents a useful tool to explore certain properties of the triplet state, especially in cases with no phosphorescence. The 'phase' of CIDNP resonances, i.e., emission or enhanced absorption, reflects the spin selectivity of electron transfer reactions. In radical ion pairs the spin selectivity is determined by the relation between the change of the standard free enthalpy DeltaG degrees during the electron back transfer and the triplet energies (E(T)) of the products. If triplet recombination is energetically feasible (DeltaG degrees > E(T)), it is typically the more efficient process in agreement with the Marcus theory.

Target-assembled tandem oligonucleotide systems based on exciplexes for detecting DNA mismatches and single nucleotide polymorphisms

We report the first exciplex-based split-probe system for DNA detection. The detector is split at a molecular level into signal-silent components which, before a signal is generated, must be assembled correctly into a particular three-dimensional arrangement. The model system comprises of two 8-mer oligonucleotides, complementary to neighbouring sites of a 16-mer DNA target, each equipped with moieties able to form an exciplex on correct, contiguous hybridization. The exciplex emits at approximately 480 nm with a large Stokes shift (135 nm). The extremely rigorous structural demands for exciplex formation and emission were achieved by careful structural design and by the discovery that high levels of certain organic solvents (especially trifluoroethanol) specifically favour emission of the DNA-mounted exciplex, probably the net result of the particular duplex structure and specific solvation of the exciplex partners. Inserts and mismatches can be effectively detected by this exciplex construct giving potential for single nucleotide polymorphism detection.

An exciplex-based, target-assembled fluorescence system with inherently low background to probe for specific nucleic acid sequences

A novel detection technique, called ExciProbes, has been developed to proof-of-principle level for DNA oligonucleotides. The new approach is based on the use of two short oligonucleotides complementary to a target nucleic acid sequence. Each short-probe oligonucleotide bears the separated parts of a new class of fluorescence detector, an exciplex. These isolated parts of the detector have no inherent signal at the detection wavelength. They are designed to detect biotarget by being assembled by the target itself to give a new molecular entity (the exciplex), with a characteristic fluorescence and very large Stokes shift (typically >150 nm). The technique is not related to fluorescence resonance energy transfer, and can potentially resolve to 1 base pair. ExciProbes can detect single or double mutations in a short sequence of DNA, and can be combined with temperature-filtering to provide allelic discrimination of single nucleotide polymorphism analysis. Compared to other fluorophore systems that have large backgrounds (typically >60%), ExciProbes show backgrounds of <1% under comparable conditions, and can be used with DNA, RNA, or synthetic nucleic acids such as locked nucleic acid.