The SPR sensor detecting cytosine[bond]cytosine mismatches

We have synthesized the first surface plasmon resonance (SPR) sensor that detects cytosine-cytosine (C[bond]C) mismatches in duplex DNA by immobilizing aminonaphthyridine dimer on the gold surface. The ligand consisting of two 2-aminonaphthyridine chromophores and an alkyl linker connecting them strongly stabilized the C[bond]C mismatches regardless of the flanking sequences. The fully matched duplexes were not stabilized at all under the same conditions. The C[bond]T, C[bond]A, and T[bond]T mismatches were also stabilized with a reduced efficiency. SPR analyses of mismatch-containing 27-mer duplexes were performed with the sensor surface on which the aminonaphthyridine dimer was immobilized. The response for the C[bond]C mismatch in 5'-GCC-3'/3'-CCG-5' was about 83 times stronger than that obtained for the fully matched duplex. The sensor successfully detects the C[bond]C mismatch at the concentration of 10 nM. SPR responses are proportional to the concentration of the C[bond]C mismatch in a range up to 200 nM. Aminonaphthyridine dimer could bind strongly to the C[bond]C mismatches having 10 possible flanking sequences with association constants in the order of 10(6) M(-1). The facile protonation of 2-aminonaphthyridine chromophore at pH 7 producing the hydrogen-bonding surface complementary to that of cytosine was most likely due to the remarkably high selectivity of 1 to the C[bond]C mismatch.     

1-methylidenesqualene and 25-methylidenesqualene as active-site probes for bacterial squalene:hopene cyclase

1-methylidenesqualene and 25-methylidenesqualene were converted to 30-methylidenehop-22(29)-ene by squalene:hopene cyclase from Alicyclobacillus acidocaldarius. It was remarkable that both analogues generated the same product. The hopanyl intermediate cation, stabilized by the methylidene residue, enabled a rotation of the isobutenyl group at C-21 prior to the final proton elimination. In contrast, in the formation of hop-22(29)-ene, the final proton abstraction takes place regiospecifically from the Z-methyl group, which was verified by cyclization of (1,1,1,24,24,24-(2)H(6))squalene into (23,23,23,30,30,30-(2)H(6))hop-22(29)-ene. [reaction: see text]     

Properties of semiconductor electrodes coated with living films of cyanobacteria

IntactPhormidium sp. cells, immobilized on a SnO₂ semiconductor electrode, are capable of transferring electrons to SnO₂ in a light-dependent reaction. Drying a “wet” algal electrode at 50°C for 60 min increases photocurrent output capacity by 100-fold. We have studied the effect of various parameters on photocurrent generation. The magnitude of the photocurrent increased with increasing light intensity and depended on the nature of the electrolyte solution. The output, about 8 μA 10 μg Chl^?1 cm⁺², was obtained using 50 mM H₃BO₃?Na₂CO₃?KCl buffer as an electrolyte, an irradiance (>460 nm) of 250 J/m², and potentiostatic conditions (the algal working electrode was poised at +0.6 V vs a saturated calomel electrode). The yield was more than doubled upon addition of an electron carrier, such as methyl viologen, benzyl viologen, or Vitamin K₃, to the electrolyte solution. Maximum photocurrent was obtained at around pH 8 and 45°C, which are optimal conditions for growth of the cyanobacterium. Furthermore, DCMU, an inhibitor of photosynthetic electron flow, drastically decreased the yield, as did heat treatment of the electrode at 110°C for 15 min. The photocurrent action spectrum peak coincided well with the absorption peak of the light-harvesting pigment, phycocyanin. These results support the idea that electron transfer can occur across algal cell walls from the source of the light-induced reactions located within the lamellar membranes to the semiconductor electrode.     

Vibrational energy redistribution in jet-cooled hydrogen-bonded phenols

Dispersed fluorescence spectra of jet-cooled hydrogen-bonded phenols have been observed by excitation of intra- and inter-molecular vibrational levels. The spectra show that vibrational energy redistribution occurs from the excited vibronic level into intermolecular vibrational modes. Energy redistribution within the intermolecular vibrational modes was also found.     

Determination of stereochemistry of bacteriochlorophyll gF and 8(1)-hydroxy-chlorophyll aF from Heliobacterium modesticaldum

The reaction center complex of heliobacteria contains three kinds of chlorophyll pigments, bacteriochlorophyll gF (BChl gF), its 13(2)-epimer BChl gF' and 8(1)-hydroxy-chlorophyll aF (8(1)-OH-Chl aF). Because the full stereochemistry of these naturally occurring chlorophyllous pigments has remained unknown, we determined the stereochemistry of both BChl gF and 8(1)-OH-Chl aF extracted from Heliobacterium modesticaldum. The configurations of the specific functional groups at ring-B as well as those at ring-D and -E were investigated by use of nuclear Overhauser effect correlations in their 1H-NMR spectra and circular dichroism spectra, as well as by modified Mosher's method in their chemical modification: (1) E-configuration was confirmed for the 8-ethylidene group at ring-B in BChl gF, (2) R-configuration was identified for the 1-hydroxyethyl group at ring-B in 8(1)-OH-Chl aF and (3) 13(2)-(R)-, 17-(S)- and 18-(S)-configurations at ring-D and -E in both BChl gF and 8(1)-OH-Chl aF were confirmed. These stereochemistries enabled us to discuss their biosynthesis and to propose possible routes for preparation of ethylidene and 1-hydroxyethyl groups at the 8-position.     

An attempt to parameterize the structuredness of solvents

An attempt has been made to parameterize the structuredness of solvents from the viewpoint of intermolecular interactions, and the structuredness parameter S _p has newly been proposed. The enthalpy of vaporization H _vap ^/o of various solvents has been considered to consist of donor-acceptor interaction energy (DA), which can been estimated from Gutmann's donor and acceptor numbers, some other interaction energies (VDW), which may not be fully described in terms of the donor-acceptor interactions and may be related to the electronic distribution, the volume and shape of the molecule, the polarizability and ionization potential of atoms in the molecule, the energies of these interactions being usually considered to be of Van der Waals type and possibly evaluated from the enthalpy of vaporization ofn-alkanes, and the intermolecular interaction energy (STR) due to the three-dimensional molecular ordering in the liquid: H _vap ^/o =DA+VDW+STR. The STR term obtained as the difference between H _vap ^/o and (DA+VDW) is defined as the structuredness parameter S _p , which is a dimensionless quantity by dividing the value with the (kJ-mol^–1) unit. The entropies of formation S ₁ ^o and S ₄ ^o of [MX]⁺ and [MX₄]^2– complexes, respectively, of divalent metal ions (Mn²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, and Hg²⁺) with halide and thiocyanate ions in aqueous and nonaqueous solvents could be represented as an almost linear function of the structuredness parameters S _p .     

Effective form of sulfoquinovosyldiacyglycerol (SQDG) vesicles for DNA polymerase inhibition

Sulfoquinovosyldiacyglycerol (SQDG) has a wide range of biological activities that make it an attractive compound for the development of new drugs. Chemically synthesized beta-SQDG-C(18:0) (1,2-di-O-stearoyl-3-O-(6-deoxy-6-sulfo-beta-d-glucopyranosyl)-sn-glycerol), for example, has a potent inhibitory effect on DNA polymerases. We investigated the properties of the vesicle form of beta-SQDG-C(18:0) as the monomer has low solubility in water. The structure of the beta-SQDG-C(18:0) vesicles are highly influenced by NaCl concentration in preparation process. At low NaCl concentrations, the beta-SQDG-C(18:0) vesicles have high surface curvature and form small unilamellar vesicles. Increases in NaCl concentration, resulted in decreased surface curvature and a tendency for beta-SQDG-C(18:0) to form large multilamellar vesicles. The small unilamellar vesicles showed a potent inhibitory effect on DNA polymerase beta, whereas the large multilamellar vesicles had no such effect. We investigated further the relationship between vesicle size and activity by preparing smaller vesicles (262, 99 and 43 nm in diameter) using an extrusion technique. These smaller vesicles had a greater inhibitory effect on DNA polymerase beta activity than non-extruded vesicles. beta-SQDG-C(18:0) vesicles, especially those of small size, were effective in DNA polymerase inhibition and are expected to have high applicability in DNA polymerase study.     

Biosynthesis of polyhydroxyalkanoate (PHA) copolymer from fructose using wild-type and laboratory-evolved PHA synthases

Eleven laboratory-evolved polyhydroxyalkanoate (PHA) synthases which originated from Pseudomonas sp. 61-3 enzyme (PhaC1(Ps)), together with the wild-type enzyme, were applied for PHA synthesis from fructose using Ralstonia eutropha PHB(-)4 as a host strain. The evolved PhaC1(Ps) mutants had amino acid substitution(s) at position 325 and/or position 481. In these mutants, serine-325 (S325) was replaced by cysteine (C) or threonine (T), while glutamine-481 (Q481) was replaced by lysine (K), methionine (M) or arginine (R). All recombinant strains harboring the genes of the evolved PhaC1(Ps) mutants produced a significantly increased amount of PHA (55-68 wt.-%) compared with the one harboring the wild-type gene (49 wt.-%). Particularly, those evolved PhaC1(Ps) mutants having multiple amino acid substitutions showed higher activities for PHA synthesis. Characterization of the PHA by NMR spectroscopy revealed that they were copolymers consisting of (R)-3-hydroxybutyrate (98-99 mol-%) and medium-chain-length comonomers (1-2 mol-%). This study also confirmed that amino acid substitution at position 481 in PhaC1(Ps) led to an increasing molecular weight of PHA. The number-average molecular weight (Mn) of PHA (Mn = 240,000) synthesized by the evolved PhaC1(Ps) (Q481K) mutant was 4.6-fold greater than that (Mn = 52,000) synthesized by the wild-type enzyme.     

Binding constants of calcium and/or magnesium electrolytes and aggregation numbers in oil-in-water type microemulsions formed by an amphoteric surfactant

The effects of anti-symmetric electrolytes (CaCl₂, Ca(SCN)₂, MgCl₂, and/or Mg(SCN)₂) and pH on the phase behavior, the -potential, the hydrodynamic diameter and the surface charge density of an oil-inwater type (O/W-type) microemulsion formed in solutions of an amphoteric surfactant (N ,N -dimethyl-N -lauroyllysine, DMLL)/n-octane/1-pentanol/brine have been examined. The formation of the microemulsion in the presence of CaCl₂ and/or Ca(SCN)₂ is of Winsor-type with an increase in the concentration of 1-pentanol. Particularly, microemulsion is not formed by the addition of Ca(SCN)₂ in a pH region less than 2.6. The -potential and the surface charge density of the microemulsion in the presence of CaCl₂ decrease with an increase in pH and show slightly positive values in the isoelectric region (pH 5-7), while, in the presence of Ca(SCN)₂, the -potential and the surface charge density show negative values in the same region at which the net charge of DMLL molecules becomes almost zero. The hydrodynamic diameters in the presence of CaCl₂ show a maximum value around pH 2.5, whereas, in the presence of Ca(SCN)₂, the minimum value is around pH 5.5. Similar tendencies are recognized in results for the -potential, the hydrodynamic diameter and the surface charge density of the O/W-type microemulsion in the presence of MgCl₂ and Mg(SCN)₂. A new formula to estimate the binding constants (K) of Ca²⁺, Mg²⁺, Cl^–, and SCN^– to the hydrophilic groups in DMLL molecules and the adsorption density of DMLL molecules on the oil/water interface (N) in the presence of antisymmetric electrolytes has been derived.K for Ca²⁺, Mg²⁺, Cl^–, and SCN^– was found to beK _Ca=0.12M^–1,K _Mg=0.14 M^–1,K _Cl=0.0084±0.0016 M^–1, respectively.N for DMLL molecules in the presence of CaCl₂, Ca(SCN)₂, MgCl₂ and/or Mg(SCN)₂ was found to be 0.50 nm^–2, 0.38 nm^–2, 0.44 nm^–2, and 0.47 nm^–2, respectively; and the surfactant (DMLL) numbers per O/W-type microemulsion droplet change from a few hundreds to a few thousands with changing pH. The larger the hydrodynamic diameter of the O/W-type microemulsion, the greater the number of DMLL molecules adsorbed on the O/W-type microemulsion surfaces.     

Synthesis of 1-aryl-5-arylazo-3-phenylsulfonylpyrazol-4-ols from 1-bromo-3-phenylsulfonyl-2-propanone

Treatment of 1-bromo-3-phenylsulfonyl-2-propanone ( 1 ) with arenediazonium chloride gave 1-aryl-5-arylazo-3-phenylsulfonylpyrazol-4-ols 5a-h in 13–48% yields.