DNA-conjugated polymers for self-assembled DNA chip fabrication.

We developed two DNA-conjugated polymers, one based on polyallylamine and the other on polyacrylic acid, for use in DNA chips. A 30-mer single-stranded DNA probe and thioctic acid were covalently attached to polyallylamine as sidechains. The same single-stranded DNA and 3-(pyridyldithio)propionyl hydrazide were covalently attached to polyacrylic acid as sidechains. Both DNA-conjugated polymers could be specifically immobilized onto a gold sensor substrate by a self-assembly technique. The interactions between fully matched DNA and each DNA-conjugated polymer were investigated by surface plasmon resonance. A gold surface modified with either DNA-conjugated polymer recognized fully matched DNA much better than unmatched DNA. The hybridization selectivity and efficiency of DNA-conjugated polyallylamine was optimized by adjusting the pH so as to reduce the effects of cationic polymer sidechains. The hybridization selectivity and efficiency of DNA-conjugated polymers were higher than those of a conventional immobilized thiol-based DNA. The coating of DNA-conjugated polymers reduced nonspecific adsorption of DNA by the gold substrate. DNA-conjugated polyacrylic acid was more selective toward fully matched DNA than was DNA-conjugated polyallylamine. Therefore, DNA-conjugated polymers show promise for application in novel DNA chips.     

Self-assembled DNA-conjugated polymer for novel DNA chip.

We developed DNA-conjugated polymer for DNA chip fabrication. A 30 mer probe DNA and disulfide bridges were covalently attached to the polymer side chain. The DNA-conjugated polymer can be specifically adsorbed on a gold substrate surface by a self-assembly technique. The interaction between fully matched DNA and DNA-conjugated polymer was investigated by surface plasmon resonance (SPR) technique. The DNA-conjugated polymer-modified gold surface highly recognized fully matched DNA, rather than unmatched DNA. Therefore, DNA-conjugated polymer can be used for novel DNA chip fabrication.     

Synthesis, properties, and crystal structure of a novel anthracene-bridged molybdenum-zinc porphyrin dimer

The synthesis and properties of novel anthracene-bridged porphyrin dimers having an oxomolybdenum(V) porphyrin unit, H(2)(DPA)[Mo(V)O(OMe)] (1) and (DPA)[Mo(V)O(OMe)][Zn(II)(MeOH)] (2), and the relevant monomer porphyrin complexes Mo(V)O(MPP)OMe (3) and Zn(II)(MPP) (4) are presented. An oxomolybdenum(V) unit was introduced into one of the two porphyrins in DPA to give 1, which has a free-base porphyrin unit. By introducing a zinc(II) ion to the free-base part, a mixed-metal complex of 2 was prepared and isolated. The structure of 2 was analyzed by X-ray crystallography (2.(7)/(6)CH(2)Cl(2), triclinic, P(-)1 (no. 2), a = 15.2854(12) A, b = 19.9640(15) A, c = 13.6915(12) A, alpha = 90.968(3), beta = 113.108(4), gamma = 96.501(4), Z = 2, R1 = 9.9, wR2 = 19.2). The structure of 2 demonstrated that a methanol is stably coordinated to the Zn(II) ion with the aid of a hydrogen bond to the methoxo ligand on the Mo(V) ion in the binding pocket of DPA. The electrochemical measurements of 2 suggested that the methanol was kept in the pocket of DPA in solution even at the reduced state of the molybdenum ion.     

DPPH (= 2,2‐Diphenyl‐1‐picrylhydrazyl = 2,2‐Diphenyl‐1‐(2,4,6‐trinitrophenyl)hydrazyl) Radical‐Scavenging Reaction of Protocatechuic Acid Esters (= 3,4‐Dihydroxybenzoates) in Alcohols: Formation of Bis‐alcohol Adduct

Protocatechuic acid esters (= 3,4‐dihydroxybenzoates) scavenge ca. 5 equiv. of radical in alcoholic solvents, whereas they consume only 2 equiv. of radical in nonalcoholic solvents. While the high radical‐scavenging activity of protocatechuic acid esters in alcoholic solvents as compared to that in nonalcoholic solvents is due to a nucleophilic addition of an alcohol molecule at C(2) of an intermediate o‐quinone structure, thus regenerating a catechol (= benzene‐1,2‐diol) structure, it is still unclear why protocatechuic acid esters scavenge more than 4 equiv. of radical (C(2) refers to the protocatechuic acid numbering). Therefore, to elucidate the oxidation mechanism beyond the formation of the C(2) alcohol adduct, 3,4‐dihydroxy‐2‐methoxybenzoic acid methyl ester ( 4 ), the C(2) MeOH adduct, which is an oxidation product of methyl protocatechuate ( 1 ) in MeOH, was oxidized by the DPPH radical (= 2,2‐diphenyl‐1‐picrylhydrazyl) or o‐chloranil (= 3,4,5,6‐tetrachlorocyclohexa‐3,5‐diene‐1,2‐dione) in CD₃OD/(D₆)acetone 3 : 1). The oxidation mixtures were directly analyzed by NMR. Oxidation with both the DPPH radical and o‐chloranil produced a C(2),C(6) bis‐methanol adduct ( 7 ), which could scavenge additional 2 equiv. of radical. Calculations of LUMO electron densities of o‐quinones corroborated the regioselective nucleophilic addition of alcohol molecules with o‐quinones. Our results strongly suggest that the regeneration of a catechol structure via a nucleophilic addition of an alcohol molecule with a o‐quinone is a key reaction for the high radical‐scavenging activity of protocatechuic acid esters in alcoholic solvents.     

Specific heat and neutron diffraction study on quaternary sulfides BaNd2CoS5 and BaNd2ZnS5

Magnetic and electrical properties are investigated for quaternary neodymium sulfides BaNd₂TS₅ (T=Co, Zn) through the specific heat, neutron diffraction, and electrical conductivity measurements. Their electrical conductivities show semiconductive behavior, which follows the Arrhenius temperature dependence with the activation energy of E_a=1.46 eV for BaNd₂ZnS₅ and E_a=1.19 eV for BaNd₂CoS₅. The specific heat of BaNd₂ZnS₅ has a λ-type anomaly at 2.8 K due to the antiferromagnetic ordering of the Nd³⁺ moments and a Schottky-type anomaly at around 60 K, which results from the crystal field splitting of the ⁴I_9/2 ground state of the Nd³⁺ ion. The specific heat of BaNd₂CoS₅ shows two λ-type anomalies at 5.7 K due to the antiferromagnetic ordering of Nd³⁺ and at 58 K due to the antiferromagnetic ordering of Co²⁺. The latter overlaps with the Schottky-type anomaly due to the crystal field splitting of the Nd³⁺ ion. Neutron diffraction measurements for BaNd₂CoS₅ show that a magnetic arrangement of the Co²⁺ moments has a collinear antiferromagnetic structure, while that of the Nd³⁺ moments has a noncollinear one.     

Duplex dissociation of telomere DNAs induced by molecular crowding

Because of the importance of telomere DNAs, the structures of these DNAs in vivo are currently of great research interest in the medical, pharmaceutical, chemical, and industrial fields. To understand the structure of biomolecules in vivo, their properties studied in vitro are extrapolated to the in vivo condition, while the condition in a living cell is inherently molecularly crowded and a nonideal solution contains various biomolecules. We investigated the effect of molecular crowding, which is one of the most important cellular environmental conditions, on the structure and stability of the telomere and G-rich and C-rich DNAs using circular dichroism (CD) spectra, CD melting curves, and isothermal titration calorimetry (ITC). The CD spectra and CD melting curves of G-rich DNA, C-rich DNA, and the 1:1 mixture of G-rich and C-rich DNAs showed that each G-rich DNA, C-rich DNA, and the 1:1 mixture form the antiparallel G-quadruplex, I-motif, and duplex, respectively, in the noncrowding condition as previously considered. On the contrary, the G-rich and C-rich DNAs individually form the parallel G-quadruplex and I-motif, respectively, in the molecular crowding condition, and the 1:1 mixture folds into the parallel G-quadruplex and I-motif but does not form a duplex. The ITC measurements indicated that the thermodynamic stability (DeltaG degrees (20)) of the duplex formation between the G-rich and C-rich DNAs in the noncrowding condition was -10.2 kcal mol(-)(1), while only a small heat change was observed in the ITC measurements in the molecular crowding condition. These ITC results also demonstrated that the molecular crowding condition prevents any duplex formation between G-rich and C-rich DNAs. These results indicate that a structural polymorphism of the telomere DNAs is induced by molecular crowding in vivo.     

Motor protein nano-biomachine powered by self-supplying ATP

A new nano-biomachine has been created from microtubules (MTs) and hetero-bifunctional polymer particles bearing pyruvate kinase, which is propelled on glass surfaces coated with kinesin by use of self-supplying ATP.     

Synthesis and photochromic properties of novel yellow developing photochromic compounds

Two 1-thiazolyl-2-thienylcyclopentene derivatives, 1a and 2a, and a 1-thiazolyl-2-vinylcyclopentene derivative 3a have been synthesized in an attempt to obtain photochromic compounds which change the color from colorless to yellow, and have low photocycloreversion quantum yields and high absorption coefficients of the colored isomers. All of these compounds underwent reversible photochromic reactions. Compounds 1a and 2a in toluene solutions changed the color upon 313 nm light irradiation from colorless to orange and pink, in which absorption maxima were observed at 494 nm (ε=10,000 M⁻¹ cm⁻¹) and 525 nm (ε=8500 M⁻¹ cm⁻¹), respectively. On the other hand, the colorless toluene solution of 3a turned yellow upon irradiation with 313 nm light, in which the absorption maximum was observed at 416 nm (ε=17,100 M⁻¹ cm⁻¹). The photocyclization/cycloreversion quantum yields of 3 were 0.19 and 0.0014, respectively. The conversion from the open- to the closed-ring isomer of 3 in the photostationary state under irradiation with 313 nm light was close to 100%.     

2-Pyridone and 3-oxo-1,2,6-thiadiazine-1,1-dioxide derivatives: a new class of hydrogen bond equivalents of uracil

Hydrogen bond complex stability between adenine (A) and hydrogen bond equivalents of uracil: 2-pyridone derivatives (U^X _X2O) and 3-oxo-1,2,6-thiadiazine-1,1-dioxide derivatives (U^X _SO2) was studied, and as the result, the hydrogen bond energy of U^X _X2O-A and a complex of UX^X _SO2-A, was about 1.5 kcal/mol more stable than that of the corresponding adenine-uracil derivatives complex, respectively. The energy difference between the imide tautomer and enol tautomer was smaller than those of uracil derivatives. U^F _SO2 can form a stable complex with A, and its imide tautomer is stable.     

Preparation of a zwitterionic trichloroplatinum(II) complex with an alkylbipyridinum ligand and its reaction in dmso-<Emphasis Type="BoldItalic">d</Emphasis><Subscript>6</Subscript> solution

A zwitterionic trichloroplatinum(II) complex PtCl₃(4,4′-bpy-N-ⁿBu) (1) was prepared by an aqueous reaction of [4,4′-bpy-N-ⁿBu]Cl with K₂PtCl₄, and was characterized by ¹H-n.m.r. and IR spectroscopy as well as elemental analysis. Dissolving (1) into dmso-d ₆ at 25 °C yields a mixture of the complexes, cis-PtCl₂(4,4′-bpy-N-ⁿBu)(dmso-d ₆) (2-cis), trans-PtCl₂(4,4′-bpy-N-ⁿBu)(dmso-d ₆) (2-trans), [4,4′-bpy-N-ⁿBu]Cl and PtCl₂(dmso-d ₆)₂. Ratio of the products in the dmso-d ₆ solution changed depending on the temperature and the total concentration of the complexes. These compounds are in equilibrium via isomerization reaction between (2-cis) and (2-trans) and via displacement reaction of the alkylbipyridinium ligand of (2-cis) and (2-trans) with dmso-d ₆ to form [4,4′-bpy-N-ⁿBu]Cl and PtCl₂(dmso-d ₆)₂.