Mariko Tarui

Mutual assistance of hydrogen-bond pairing and aromatic stacking interactions for molecular recognition: Spectroscopic study on the interaction of guanine base with cytosine and tryptophan molecules

Fluorescence and 1H-NMR spectroscopic experiments on the interaction of guanine base with cytosine base and Trp indole ring using the model compounds have shown the first clear-cut evidence that both of the hydrogen-bond pairing and aromatic stacking interactions, which are recognized as important forces for the strict molecular recognition, do not function independently, but highly help each other for the recognition of guest molecule.

Enhancement of aromatic amino acid-nucleic acid base stacking interaction by metal coordination to base: fluorescence study on a tryptophan-Pt(II)-guanine ternary complex

In order to investigate the effect of the Pt(II) ion on the stacking interaction between tryptophan and a guanine base, the quenching of Trp fluorescence was monitored for some systems in the absence and presence of the metal ion, and the association constants were obtained by the analysis of Eadie-Hofstee plots. All spectral data suggested that the stacking interaction is enhanced by the Pt(II) coordination to the guanine N7 atom. The result indicates the importance of the metal ion as a bookmark in the specific recognition of a nucleic acid base by an aromatic amino acid residue.In order to investigate the effect of the Pt(II) ion on the stacking interaction between tryptophan and a guanine base, the quenching of Trp fluorescence was monitored for some systems in the absence and presence of the metal ion, and the association constants were obtained by the analysis of Eadie‐Hofstee plots. All spectral data suggested that the stacking interaction is enhanced by the Pt(II) coordination to the guanine N7 atom. The result indicates the importance of the metal ion as a bookmark in the specific recognition of a nucleic acid base by an aromatic amino acid residue.

Interaction of mutagenic tryptophan pyrolysate with DNA. CD spectral study on the binding specificity.

The interactions of DNA duplexes with 3‐amino 1,4‐dimethyl‐5H‐pyrido[4,3‐b]indole(Trp‐P‐1), a potent mutacarcinogen isolated from tryptophan pyrolysate, have been studied using CD spectroscopy. The results are that (a) the spectral change of B‐form DNA caused by the interaction with Trp‐P‐1 is biphasic, i.e. the enlargement of CD bands characteristic to the B‐DNA conformation in the range of r ([Trp‐P‐1]/[DNA]) = 0–2.5, followed by the rapid transition to the non‐B conformation at r > 2.5; (b) this transition degree of B to non‐B conformation of DNA is not necessarily dependent on the G‐C content; and (c) the salt‐induced Z‐DNA is transformed to B‐DNA (0 < r < 0.1) and then to non‐B‐DNA (r > 5), depending on the concentration of Trp‐P‐1 added. These data indicate that the non‐covalent interaction of Trp‐P‐1 with DNA is mainly dependent on the B‐DNA conformation.

Cooperative face-to-face and edge-to-face aromatic interactions of tryptophan indole ring with N7-quarternized guanine and neutral cytosine bases

In order to investigate the effect of cytosine base upon the stacking interaction of N7‐quarternized guanine base with tryptophan indole ring, the X‐ray crystal structure of a 1:1 complex of model compounds 1 and 2 was carried out. Contrary to the expectation of the interaction of both molecules in aqueous solution, the crystal structure showed the first example of the simultaneous recognition of the Trp indole ring by guanine and cytosine bases by the coupling of the face‐to‐face and edge‐to‐face aromatic interactions, respectively.

N-[3-(Cytosin-1-yl)propionyl]-l-isoleucine, a heavily hydrated structure with four cytosine–isoleucine hybrids in the asymmetric unit

A hybrid molecule, N-[3-(4-amino-1,2-dihydro-2-oxopyrimidin-1-yl)propionyl]-L-isoleucine (C-Ile), was crystallized with four cytosine-isoleucine hybrid molecules and 9.5 waters of hydration in the asymmetric unit, i.e. 4C 13 H 20 N 4 O 4 .9.5H 2 O. The conformations of the four independent C-Ile molecules are similar, but not identical. They are interconnected by hydrogen bonds, many of which involve bridging solvent molecules.

A Cytosine and Tryptophan Hybrid Dipeptide: Cytosinyl-l-tryptophan–Water (2/6)

The hybrid dipeptide of the title compound, 2C 18 H 19 N 5 O 4 .6H 2 O, containing cytosine base and L-tryptophan was crystallized in hexahydrated form; the solvent occupies 12% by weight of the asymmetric unit. Two independent molecules were distinguished by the different directions of their indole rings. All polar atoms of the title compound participate in hydrogen-bond formation, and a tight network is built by combination with solvent-mediated hydrogen bonds. A π-π electron interaction was observed between the indole and nucleic base; it is facilitated by hydrogen bonds.