Seiichi Nishizawa

Strong hydrogen bond-mediated complexation of H2PO4− by neutral bis-thiourea hosts

Abstract Highly preorganized bis-thiourea receptors based on a xanthene spacer selectively (H2PO4− > CH3COO− > Cl−) bind dihyrogenphosphate via multitopic hydrogen bonding, giving stronger complexes with H2PO4− neutral receptor known so far. The high complexation strengths are rationalized by the hydrogen bond donor strength of the thiourea groups and by host preorganization. The hydrogen acceptor strengths of the guest anions and, for small ions, guest solvation explain the observed selectivity of complexation in dimethyl sulfoxide (DMSO).

Anion recognition by urea and thiourea groups: Remarkably simple neutral receptors for dihydrogenphosphate

A bis-urea and a bis-thiourea host, both derived in only one step from 1,3-bis(aminomethyl)benzene, are shown to bind dihydrogenphosphate selectively over various other anions (H2PO4− > CH3COO− > Cl− > HSO4− > NO3− > ClO4−). The much stronger binding of H2PO4− by the bis-thiourea is rationalized by the stronger H-bond donor strength of the thiourea groups and the binding selectivity is explained in terms of the complex geometry and the basicity of the guest anions. The lack of self-association and the changes in the UV spectrum upon complexation make bis-thiourea hosts a promising new class of neutral receptors for dihydrogenphosphate.

A thiourea-based chromoionophore for selective binding and sensing of acetate

Abstract Highly selective binding and sensing of acetate over various monovalent inorganic anions (MeCO 2 − ≫H 2 PO 4 − >Cl − , Br − , I − , SCN − , NO 3 − , HSO 4 − , ClO 4 − ) are achieved by N , N ′-bis( p -nitrophenyl)thiourea as a hydrogen-bonding chromoionophore in 1% water–99% MeCN (v/v), and acetic acid in vinegar is successfully determined by the complexation-induced chromogenic response of this chromoionophore.

Influence of substituent modifications on the binding of 2-amino-1,8-naphthyridines to cytosine opposite an AP site in DNA duplexes: thermodynamic characterization

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.

Cooperative DNA Probing Using a β-Cyclodextrin−DNA Conjugate and a Nucleobase-Specific Fluorescent Ligand

A single nucleotide polymorphism (SNP) base on the target is displayed at a gap in a ternary duplex carrying beta-cyclodextrin-modified DNA. A stable tandem duplex forms regardless of the type of SNP base. A nucleobase-specific ligand is then added to this system. The dansyl moiety in the ligand is expected to form a luminous inclusion complex with nearby beta-CyD, only when the ligand recognizes the specific base displayed in the gap.

Fluorescence detection of guanine–adenine transition by a hydrogen bond forming small compound

In combination with abasic site-containing oligodeoxynucleotides, 2-amino-4-oxopteridine (pterin) can selectively recognize guanine base over other nucleobases accompanied by fluorescence quenching, which allows clear detection of a guanine-adenine transition with the naked eye.

Fluorescence detection of cytosine/guanine transversion based on a hydrogen bond forming ligand

In combination with abasic site (AP site)-containing oligodeoxynucleotides (ODNs), we demonstrate potential use of a hydrogen bond forming ligand, 2-amino-7-methyl-1,8-naphthyridine (AMND), for the fluorescence detection of the cytosine (C)/guanine (G) mutation sequence of the cancer repression gene p53. Our method is based on construction of the AP site in ODN duplexes, which allows small synthetic ligands to bind to target nucleobases accompanied by fluorescence signaling: an AP site-containing ODN is hybridized with a target ODN so as to place the AP site toward a target nucleobase, by which hydrophobic microenvironments are provided for ligands to recognize target nucleobases through hydrogen-bonding. In 10mM sodium cacodylate buffer solutions (pH, 7.0) containing 100mM NaCl and 1.0mM EDTA, AMND is found to strongly bind to C (K(d)=1.5x10(-6)M) in the target ODN while the binding affinity for G is relatively moderate (K(d)=50x10(-6)M). Significant fluorescence quenching of AMND is observed only when binding to C, making it possible to judge the C/G transversion with the naked eye.

Strong and Selective Binding of Amiloride to an Abasic Site in RNA Duplexes: Thermodynamic Characterization and MicroRNA Detection

Firmly tied: The binding affinity of amiloride for an abasic (AP) site-containing RNA duplex is two orders of magnitude superior to the affinity of the corresponding AP site-containing DNA duplex. The observed high binding affinity for the RNA duplex arises from a favorable enthalpy gain. The binding-induced fluorescence response of amiloride is applicable to microRNA detection.

Effect of the bases flanking an abasic site on the recognition of nucleobase by amiloride

BACKGROUND We explain here the various non-covalent interactions which are responsible for the different binding modes of a small ligand with DNA. METHODS The combination of experimental and theoretical methods was used. RESULTS The interaction of amiloride with thymine was found to depend on the bases flanking the AP site and different binding modes were observed for different flanking bases. Molecular modeling, absorption studies and binding constant measurements support for the different binding patterns. The flanking base dependent recognition of AP site phosphates was investigated by (31)P NMR experiments. The thermodynamics of the ligand-nucleotide interaction was demonstrated by isothermal titration calorimetry. The emission behavior of amiloride was found to depend on the bases flanking the AP site. Amiloride photophysics in the context of AP-site containing DNA is investigated by time-dependent density functional theory. CONCLUSIONS Flanking bases affect the ground and excited electronic states of amiloride when binding to AP site, which causes flanking base-dependent fluorescence signaling. GENERAL SIGNIFICANCE The various noncovalent interactions have been well characterized for the determination of nucleic acid structure and dynamics, and protein-DNA interactions. However, these are not clear for the DNA-small molecule interactions and we believe that our studies will bring a new insight into such phenomena.

Small-molecule binding at an abasic site of DNA: strong binding of lumiflavin for improved recognition of thymine-related single nucleotide polymorphisms.

The binding behavior of lumiflavin, a biologically vital ligand, with DNA duplexes containing an abasic (AP) site and various target nucleobases opposite the AP site is studied. Lumiflavin binds selectively to thymine (T) opposite the AP site in a DNA duplex over other nucleobases. Using 1H NMR spectroscopy and fluorescence measurements, we show that ligand-DNA complexation takes place by hydrogen-bond formation between the ligand and the target nucleobases and by stacking interactions between the ligand and the nucleobases flanking the AP site. From isothermal titration calorimetric experiments, we find that ligand incorporation into the AP sites is primarily enthalpy-driven. Examination of ionic strength dependency of ligand binding with DNA reveals that ligand-DNA complexation is a manifestation of both electrostatic and nonelectrostatic interactions and that the contribution from the nonelectrolyte effect is fundamental for the stabilization of the ligand-DNA complex. In comparison to riboflavin, reported previously as a T-selective ligand, lumiflavin binds to the DNA much more strongly and is a more promising ligand for efficient detection of T-related single nucleotide polymorphisms.