In mimicry of biological systems such as DNA, the fabrication of molecular assemblies and supramolecular arrays is one of the current research topics in supramolecular chemistry. 1 A wide variety of abiotic self-assembling systems such as catenanes and double helices have been described. 1 Additionally, artificial selfassembled receptors, where their substrate binding sites or cavities are organized by metal templation 2 or by self-association of monomeric ligands, 3 have been proposed to bind target substrates. The self-assembly of a receptor monolayer with a biomolecule such as ATP at the air-water interface has also been reported. 4 As a novel example of self-assembly for optical ion sensing, a K + ion-induced self-assembly has been described which consists of pyrene-tethered benzo-15-crown-5, γ-cyclodextrin, and K + ion. 5 This ternary complex, formed in water with high selectivity and sensitivity for K + , can be probed by pyrene dimer emission. 5 Thus, it is expected that the self-assembly of a chromophore-tethered receptor 6 by specific substrate binding offers a novel approach to the sensing of substrates in solution.Here we report a particularly simple self-assembling system for sensing of anions, with a pyrene-functionalized monoguanidinium receptor 1. The assembled system was quantitatively analyzed by means of 1 H NMR and fluorescence measurements. Although little attention has been paid to the structural analysis of such molecular assemblies, 7 determination of stoichiometry and structure is essential for understanding the photophysical origin of fluorescence and for making a rational design of a sensing system to distinguish structurally related substrates. The receptor 1 was found to self-assemble to form a 2:1 (host:guest) complex with high selectivity for biologically relevant pyrophosphate 8 (P 2 O 7 4-, PPi) in MeOH. From the complexation-induced changes in chemical shifts of the pyrenyl protons of 1, it is concluded that a sandwich-like ground-state pyrene dimer is present in the self-assembly. Formation of the self-assembly results in a remarkable change in the ratio of emission intensities of excimer to monomer due to the pyrenyl moiety of 1. It should be noted that only when the self-assembly is formed does 1 show a change in fluorescence spectrum. The present system, therefore, shows high selectivity for PPi that can promote formation of the self-assembly. In addition, calibration via ratiometry becomes possible by exploiting both monomer and excimer emissions. For anionic species, such emission ratio sensing has been known in only a few instances, 8b,9a despite its importance from a practical viewpoint.1 was synthesized by reacting 1-pyrenemethylamine hydrochloride with 3,5-dimethylpyrazole-1-carboxamidine nitrate in THF. Recrystallization from THF/MeOH gave 1 as nitrate salt. 10 The effect of anions on the fluorescence spectrum of 1 (8.0 × 10 -4 M) was examined in MeOH, 11 and the results are shown in Figure 1. Spectrum a was measured in the absence of anions, where 1 showed a structur...

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Nucleobase recognition in water is successfully achieved by the use of an abasic site (AP site) as the molecular recognition field. We intentionally construct the AP site in DNA duplex so as to orient the AP site toward a target nucleobase and examine the complexation of 2-amino-7-methylnaphthyridine (AMND) with nucleobases at the AP site. AMND is found to selectively bind to cytosine (C) base with a 1:1 binding constant of >106 M-1, accompanied by remarkable quenching of its fluorescence. In addition to hydrogen bonding, a stacking interaction with nucleobases flanking the AP site seems responsible for the binding properties of AMND at the AP site. Possible use of AMND is also presented for selective and visible detection of a single-base alternation related to the cytosine base.

A chloride-selective solvent polymeric membrane electrode based on a neutral hydrogen bond forming ionophore, poly(vinyl chloride) (PVC), the plasticizer 2-nitrophenyl octyl ether (o-NPOE), and cationic sites (50 mol %, relative to the ionophore) is described. At pH 7.0 (HEPES buffer), this electrode responds to chloride in a linear range from 10-5 to 10-2 M with a slope of (−54.0 ± 1.0) mV/decade and a detection limit of (6.5 ± 3.0) × 10-6 M. As compared to conventional anion-exchanger electrodes, the interference of SCN-, Br-, NO3 -, I-, and even salicylate is considerably reduced, as shown by the selectivity coefficients determined with the matched potential method (MPM) in the chloride concentration range 10-2.34−10-2.04 M (log (MPM):  Sal-, +1.8; SCN-, +1.6; NO3 -, +0.7; I-, +0.5; Br-, +0.4). Because the discrimination of the more hydrophilic anions SO4 2-, HSO3 -/SO3 2-, OAc-, HCO3 -, and H2PO4 -/HPO4 2- is too large for a determination of accurate selectivity coefficients in this high chloride concentration range, corresponding values for the range 10-5.00−10-4.70 M Cl- have been determined (log (MPM):  SO4 2-, −1.2; HSO3 -/SO3 2-, −2.0; OAc-, −2.3; HCO3 -, −2.6; H2PO4 -/HPO4 2-, < −3.5), showing here, too, a good selectivity for Cl-. The chloride ion concentration in certified control horse serum was determined by the standard addition method as 102.1 mM with a coefficient of variation of 0.42% (n = 6). This result is in excellent agreement with the certified value of 102.3 mM, as determined by coulometry, and demonstrates the applicability of this sensor for measurements in biological samples. The selectivity upon storage of the electrode in buffer solution for 4 weeks decreases but is still considerably better than that for a freshly prepared anion-exchanger electrode.

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Here, we report on a significant effect of substitutions on the binding affinity of a series of 2-amino-1,8-naphthyridines, i.e., 2-amino-1,8-naphthyridine (AND), 2-amino-7-methyl-1,8-naphthyridine (AMND), 2-amino-5,7-dimethyl-1,8-naphthyridine (ADMND) and 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), all of which can bind to cytosine opposite an AP site in DNA duplexes. Fluorescence titration experiments show that the binding affinity for cytosine is effectively enhanced by the introduction of methyl groups to the naphthyridine ring, and the 1:1 binding constant (106 M−1) follows in the order of AND (0.30) < AMND (2.7) < ADMND (6.1) < ATMND (19) in solutions containing 110 mM Na+ (pH 7.0, at 20°C). The thermodynamic parameters obtained by isothermal titration calorimetry experiments indicate that the introduction of methyl groups effectively reduces the loss of binding entropy, which is indeed responsible for the increase in the binding affinity. The heat capacity change (ΔCp), as determined from temperature dependence of the binding enthalpy, is found to be significantly different between AND (−161 cal/mol K) and ATMND (−217 cal/mol K). The hydrophobic contribution appears to be a key force to explain the observed effect of substitutions on the binding affinity when the observed binding free energy (ΔGobs) is dissected into its component terms.

We have developed a new fluorescent sensing probe for double-stranded RNA (dsRNA) by integrating thiazole orange (TO) as a base surrogate into triplex-forming PNA. Our probe forms the thermally stable triplex with the target dsRNA at acidic pH; and the triplex formation is accompanied by the remarkable light-up response of the TO unit. The binding of our probe to the target dsRNA proceeds very rapidly, allowing real-time monitoring of the triplex formation. Importantly, we found the TO base surrogate in our probe functions as a universal base for the base pair opposite the TO unit in the triplex formation. Furthermore, the TO unit is significantly more responsive for the fully matched dsRNA sequence compared to the mismatch-containing sequences, which enables the analysis of the target dsRNA sequence at the single-base pair resolution. The binding and sensing functions of our probe are described for the development of fluorescent probes applicable to sensing biologically relevant dsRNA.

Attenuated total reflectance infrared spectroscopy (ATR-IR) has been used to study the cation permselectivity of liquid-membrane ionselective electrodes (ISEs). All spectroscopic evidence was found to agree with the interpretation of permselectivity as being due to complete exclusion of counter-ions from the boundary phase. Compared to ATR-IR, optical second harmonic generation (SHG) has an even more pronounced surface sensitivity. It has been demonstrated to be a promising new technique for the study of ISE response mechanisms, as it allows one to observe the actual phase boundary. On the other hand, further potentiometric evidence for the influence of ionic sites on the emf response was found, both by a study of membranes free of ionic sites as well as by the investigation of leaching processes at poly(viny1 chloride) membranes. Finally, the use of a photoresponsive crown ether ionophore allowed the determination of emf response characteristics in relation to the ionophore concentration without any changes in the membrane composition.