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.     

Rate constants for the reactions of a series of alkylperoxy radicals with NO

The rate constants for the gas-phase reactions of isopropyl- and tert-butylperoxy radicals with nitric oxide (NO) have been studied at 298 +/- 2 K and a total pressure of 3-4 Torr (He buffer) using a laser flash photolysis technique coupled with a time-resolved negative-ionization mass spectrometry. The alkyl peroxy radicals were generated by the reaction of alkyl radicals with excess O(2), where alkyl radicals were prepared by laser photolysis of several precursor molecules. The rate constants were determined to be k(i-C(3)H(7)O(2) + NO) = (8.0 +/- 1.5) x 10(-12) and k(t-C(4)H(9)O(2) + NO) = (8.6 +/- 1.4) x 10(-12) cm(3) molecule(-1) s(-1). The results in combination with our previous studies are discussed in terms of the systematic reactivity of alkyl peroxy radicals toward NO.     

Diacetoxylation of conjugated dienes with thallium(III) acetate in acetic acid

The reaction of conjugated dienes such as 1,3-butadiene, isoprene, 2,3-dimethyl-1,3-butadiene, 2,5-dimethyl-2,4-hexadiene, 1,3-cyclopentadiene, and 1,3-cyclohexadiene, with thallium(III)acetate in acetic acid at 10–65° for 0.5–15 hr affords an isomeric mixture of the corresponding diacetoxyalkenes (1,2- and 1,4-addition products) in 10–92% yields. The 1,2-addition products are predominantly formed in all cases examined except the case of 1,3-cyclopentadiene. The reaction is assumed to proceed through acetoxythallation and dethallation steps, the latter step being accompanied and/or followed by an attack of acetoxyl group. An initial attack of thallium moiety is proposed to occur mainly at C-1 and C-2 carbons in the cases of linear terminal dienes and cyclic dienes, respectively.     

Synthesis, structure and thermal stability of fully hydrophobic porphyrin-DNA conjugates

The DNAs modified with tetraphenyl porphyrin at the center of 13mer oligonucleotide were synthesized using phosphoramidite chemistry and automated DNA synthesis. When the porphyrin modified oligonucleotide was annealed with its complementary strand, they formed a standard B-form duplex. The porphyrin moiety intercalated in the duplex, and moderately lowered the thermal stability.     

Preparation of Metallaiminophosphoranes and Their Reactivity

Treatment of [Cp*(CO) 2 M{P(NHPh)(OMe) 2 }]PF 6 (M = Fe and Ru) with NaNH 2 gives metallaiminophosphoranes, Cp*(CO) 2 M{P(NPh)(OMe) 2 }. The x-ray structures and reactivity of the complexes are reported.     

Carbon-13 NMR spectra of all-trans-N-retinylidene-n-butylamine as an analogue of the Schiff's base linkage-compound in visual pigment

Carbon-13 NMR spectra have been obtained for all-trans-N-retinylidene-n-butylamine as an analogue of the Schiff's base linkage compound in visual pigment. The chemical shift changes on going from all-trans-retinal₁ to all-trans-N-retinylidene-n-butylamine are observed. These changes indicate the collapse of the bond alternation in conjugated polyene carbons, whereas N-protonation in all-trans-N-retinylidene-n-butylamine does not affect the bond alternation.     

Ab initio molecular orbital calculations of the cobalt porphine complex. I. LCAO SCF MO calculation of low-spin,high-spin,and π-ionized states of Co-porphine

Ab initio LCAO SCF MO calculations are carried out on planar Co-porphine with a basis set of roughly double zeta quality for Co and N and of single zeta quality for C and H. The net charge on Co and N and the overlap population between them are 1.78, ?0.57, and 0.06, respectively, in the ²A_1g, state, which is known to be the ground state by experiment. The bonding in this complex is thus largely ionic. The first and second calculated ionization potentials are 6.51 and 6.77 eV, respectively, and are in reasonable agreement with the observed ionization potentials of 6.44 and 6.62 eV for Ni-tetraphenylporphine. CI calculations within the framework of the ligand field theory are also performed. The calculated order of the five lowest states is ⁴B_2g ≈ ⁴E_g, ⁴A_2g, ²A_1g, ⁴E_g from below and is not in agreement with the semiempirical order of ²A_1g ≈ ⁴B_2G, ⁴A_2g, ²E_g, ⁴E_g determined by Lin.     

Observation of the effects of radially sheared electric fields on the suppression of turbulent vortex structures and the associated transverse loss in GAMMA 10

Vortexlike turbulent structures in hot-ion mode plasmas with several keV are observed in the case with a radially produced weak shear of electric fields E(r). However, a strong E(r) shear formation due to a high ion-confining potential phi(c) production clears up these vortices together with plasma-confinement improvement and disappearance of both drift-wave and turbulencelike Fourier spectral signals. These findings are based on three-time progress in phi(c) in comparison to phi(c) attained 1992-2002. The significant advance of phi(c) is well extended in line with proposed potential-formation physics scalings.