Click chemistry to construct fluorescent oligonucleotides for DNA sequencing

"Click chemistry" 1,3-dipolar cycloaddition between alkynyl 6-carboxyfluorescein (FAM) and azido-labeled single-stranded (ss) DNA was carried out under aqueous conditions to produce FAM-labeled ssDNA in quantitative yield. The FAM-labeled ssDNA was successfully used as a primer to produce DNA sequencing products with single-base resolution in a capillary electrophoresis DNA sequencer with laser-induced fluorescence detection.     

Chromatographic separation and mass spectrometric identification of positional isomers of polyethylene glycol-modified growth hormone-releasing factor (1-29)

A one-step chromatographic method capable of separating all isomers of polyethylene glycol (PEG)-growth hormone-releasing factor (GRF) (1-29) conjugates was developed. The unmodified GRF (1-29) and seven different isomers of PEG-GRF (1-29) conjugates were separated by using a simple reversed-phase HPLC method depending on the differences of hydrophobicity due to the number and site of PEG attachment. The PEGylation sites of all isomers of PEG-GRF (1-29) conjugates were identified by determining the molecular masses of the Lys-C digested fragments with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This study is a first report for the separation of all PEG-conjugate isomers and would be useful for further studies to find the promising conjugate by evaluating biological activity and stability of each isomer.     

Azido- or hydroxyl-capped half-cubanes containing Cp*Rh fragments: [Cp*3Rh3(mu-X)3(mu3-X)]2+ (X-=OH- or N3-)

Treatment of [Cp*Rh(H(2)O)(3)](OTf)(2) (1) with Me(3)SiNH-t-Bu in acetone gave a hydroxyl-capped half-cubane [Cp*(3)Rh(3)(mu-OH)(3)(mu(3)-OH)](OTf)(3)(t-BuNH(3)) (2). Slow diffusion of Me(3)SiN(3) in diethyl ether into compound in acetone produced an azido-capped half-cubane [Cp*(3)Rh(3)(mu-N(3))(3)(mu(3)-N(3))](OTf)(2) (3). On the other hand, treating 1 with Me(3)SiN(3) in acetone gave an azido-bridged, dinuclear rhodium(III) complex [Cp*Rh(mu-N(3))(OH(2))](2)(OTf)(2) (4). Complexes 2 and 3 represent the first azido- or hydroxyl-capped, incomplete cubane-type Rh clusters. Under appropriate conditions, complexes 2 and 3 could be converted to complex 4. The structures of all products were determined by X-ray diffraction.     

Biomimetic alcohol oxidations by an iron(III) porphyrin complex: relevance to cytochrome P-450 catalytic oxidation and involvement of the two-state radical rebound mechanism

The systematic oxidation reactions of a wide range of alcohols have been carried out by using an iron porphyrin complex in order to understand their relation to cytochrome P-450 enzymes and to have a practical application to organic synthesis. The iron porphyrin complex catalyzed efficiently alcohol oxidation to the respective carbonyl compound via a high-valent iron-oxo porphyrin intermediate ((Porp)Fe=O+). Several mechanistic studies such as isotope 18O labeling, deuterium isotope effect, linear free energy relationship, and ring-opening of radical clock substrate, have suggested that the alcohol is oxidized by a sequence of reactions involving an alpha-hydroxyalkyl radical intermediate and oxygen rebound to form the gem-diol, dehydration of which yields the carbonyl compounds. Moreover, it has been proposed that a two-state reactivity mechanism can also be adopted for alcohol oxidation reactions in iron porphyrin model systems as exhibited by P-450 enzymes.     

Magnetic couplings in vanadium aromatic sandwich complexes and their crystals by using DFT methods

Using density functional theory, we have theoretically studied the origin of ferromagnetic coupling of spins in the long multiple deckers of vanadium sandwich complexes with benzene (Bz). This is done by calculating the band structure of their infinite one-dimensional (1D) crystals along the periodic (=Z) direction. We find that the magnetic coupling can be ascribed to spin polarization in the band (= those derived from d(z2)) whose k states are not involved in the formation of partial covalent bonds between vanadium atoms and benzene rings. We have also studied magnetic and electronic properties of multiple deckers of a naphthalene (Np)-vanadium complex. We find that there is a stronger covalent interaction as well as a stronger electrostatic interaction between V and Np rings than between V and Bz rings. This suggests that there is a possibility of longer multiple deckers of a Np-V complex. In addition, ferrimagnetic coupling of spins is expected, resulting in a magnetic moment 45% larger than that of the Bz-V complex at the same length. For their 1D crystals, band structure analysis also shows that the origin of magnetic coupling in long multiple deckers should be similar to that of Bz-V multiple deckers.     

The 2-(4-trifluoromethylphenylsulfonyl)ethoxycarbonyl (Tsc) amino-protecting group: use in the solid-phase synthesis of pyrrole-imidazole polyamides

The development of the 2-(4-trifluoromethylphenylsulfonyl)ethoxycarbonyl (Tsc) function, a novel base-sensitive amino-protecting group, and its application to the preparation of DNA-binding polyamides are described. Pyrrole-imidazole polyamides were synthesized by an efficient solid-phase method under conditions compatible with Fmoc chemistry using two Tsc-protected amino acids, Tsc-Py-OH 1a and Tsc-Im-OH 1b.     

Theoretical studies on the mechanism of acid-promoted hydrolysis of N-formylaziridine in comparison with formamide

[reaction: see text] We present an ab initio study of the acid-promoted hydrolysis reaction mechanism of N-formylaziridine in comparison with formamide. Since the rate of amide hydrolysis reactions depends on the formation of the tetrahedral intermediate, we focused our attention mainly on the reactant complex, the tetrahedral intermediate, and the transition state connecting these two stationary points. Geometries were optimized using the density functional theory, and the energetics were refined using ab initio theory including electron correlation. Solvent effects were investigated by using polarizable continuum method calculations. The proton-transfer reaction between the O-protonated and N-protonated amides was investigated. In acidic media, despite that the N-protonated species is more stable than the O-protonated one, it is predicted that both N-protonated and O-protonated pathways compete in the hydrolysis reaction of N-formylaziridine.     

1,3-Dipolar cycloaddition of azides with electron-deficient alkynes under mild condition in water

We report a simple synthetic protocol for the 1,3-dipolar cycloaddition of azides with electron-deficient alkynes. Alkyne with at least one neighboring electron-withdrawing group proceeds with the cycloaddition successfully without any catalysts at room temperature in water. Under this simple condition, we evaluated a series of small molecule model reactions and then coupled an azido-DNA molecule with electron-deficient alkynes for the formation of [1,2,3]-triazole heterocycle, providing a potential method for introducing functional groups to DNA under biological conditions.     

A rhodium‐catalyzed route for oxidative coupling and cyclization of 2‐aminobenzyl alcohol with ketones leading to quinolines

2‐Aminobenzyl alcohol undergoes oxidative cyclization with aryl(alkyl), alkyl(alkyl) and cyclic ketones in dioxane at 80° in the presence of a catalytic amount of RhCl(PPh₃)₃ along with KOH to afford the corresponding quinolines in good yields. The catalytic pathway seems to be proceeded via a sequence involving initial oxidation of 2‐aminobenzyl alcohol to 2‐aminobenzaldehyde by a rhodium catalyst, cross aldol reaction between 2‐aminobenzaldehyde and ketones, and cyclodehydration.