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

Abstract

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.

Benzannulated Cycloheptanones from Binaphthyl Platforms

“…[16] The excitation transfer between the donor and acceptor moieties thus most plausibly occurred through intermolecular interactions between two exci-partners. In fact, all the ketones seem to behave as two structurally independent units.…”

Target-assembled exciplexes based on Scorpion oligonucleotides

“…The Scorpion target alone showed no exciplex peak at 466 nm in the absence of Exciprobe-3 -N. The addition of Exciprobe-3 -N to the Scorpion target caused a 2-4 nm red shift of the pyrene LES emission, accompanied by its quenching. A new structureless band appeared at ∼466 nm (Figure 3), which is characteristic of a naphthalene-pyrene exciplex [7][8][9][10]. Exciplex emission is achievable due to interaction of the exci-partners on duplex formation if they are perfectly located close to one another.…”

“…For the full Scorpion system, exciplex emission in the presence of TFE was strongest at 32 % (v/v) TFE. Thus the precise structural nature of the (local) duplex formed in the Scorpion exciprobe stem-loop differs from conventional linear duplex DNA, for which exciplex mission is optimal at 80 % (v/v) TFE [7][8][9][10]. The role of TFE in allowing exciplex emission for nucleic acid systems is under investigation [7][8][9][10], but clearly the optimal conformation of the nucleic acid system (whether linear or Scorpion stem-loop) is critical as the optimal percentage of TFE varies with the system [7][8][9][10], and in organic model exciplexes TFE fully quenches exciplex emission [9].…”

“…Abbreviations used: exci-partner, exciplex partner; Exciprobe-3 -N, 3 -naphthalenyl-labelled Exciprobe; Exciprobe-3 -p, 3 -phosphate-labelled Exciprobe; Exciprobe-3 -PY, 3 -pyrene-labelled Exciprobe; LES, locally excited state; Scorpion-5 -N, 5 -naphthalenyl-labelled Scorpion; Scorpion-5 -p, 5 -phosphate-labelled Scorpion; Scorpion-5 -PY, 5 -pyrene-labelled Scorpion; TFE, trifluoroethanol; T m, 'melting' temperature of DNA; Tris buffer, 10 mM Tris/0.1 M NaCl (pH 8 A recent approach [7][8][9][10] to diminish background fluorescence uses exciplexes assembled from components that hybridize at the target sequence. This end-point exciplex method uses two components that are weakly or non-fluorescent at the detection wavelength, resulting in background fluorescence of <1 %.…”

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

“…Specific examples of pyrene-modified oligonucleotides reviewed here include sensitive fluorescent probes for the sequence-specific detection of nucleic acids (NAs) and discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors for the detection of a wide range of various targets, agents for binding of dsDNAs, building units of supramolecular complexes, and other applications. These simple synthetically-accessible molecules integrate an excellent recognition capability of oligonucleotides and ability of pyrene to act as microenvironment-sensitive fluorescent label [ 1 , 2 , 3 , 4 ], excimer- or exciplex-generating molecule [ 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ], NA complex intercalator [ 16 , 17 , 18 , 19 ], or π-π-staking hydrophobic moiety [ 20 , 21 ]. It is worth noting that these functions of pyrene are especially brightly expressed in the NA context.…”