On-chip fraction collection for multiple selected ssDNA fragments using isolated extraction channels

High efficiency and high-purity fraction collection is highly sought in analysis of fragments-of-interest from selective polymerase chain reaction (PCR) products generated by High Coverage Gene Expression Profiling (HiCEP) methods. Here we demonstrate a new electrophoretic chip device enabling automatic high-efficient fractionation of multiple ssDNA target fragments during a run of separation. We used thoroughly isolated extraction channels for each selected target to reduce the risk of cross-contamination between targets due to cross-talk of extraction channels. Fragments of 35, 108 and 138 b, were successfully isolated, then the recovery was PCR-amplified and assessed by capillary electrophoresis (CE) analysis. Total impurity level of the targets due to unwanted fragments of 0.7%, 2% and 6% respectively, was estimated. Difficulties in collecting multiple target factions are due to band diffusion and DNA adsorption to the walls for the fragments in the separation channel, which is generated by transferring the DNA target fraction from the extraction section to the target reservoir. Therefore, we have carefully measured band broadening and analyzed its influence on the separation resolution due to the delay.     

Polyrotaxane derivatives. II. Preparation and characterization of ionic polyrotaxanes and ionic slide‐ring gels

Four types of ionic polyrotaxane (PR) derivatives, that is, carboxymethylated, sulfoethylated, diethylaminoethylated, and trimethylammoniohydroxypropylated PRs, were successfully prepared starting from the same PR consisting of poly(ethylene glycol) as an axis and α‐cyclodextrins as ring molecules. The structures of the ionic PR derivatives were analyzed by ¹H and ¹³C nuclear magnetic resonance (NMR), attenuated‐total reflection Fourier transform‐infrared, and colloidal titration. Degrees of substitution of the ionic PRs were calculated from results of ¹H NMR and colloidal titrations; both sets of results satisfactorily agreed. Cross‐linking of sulfoethylated and quaternized PRs yielded ionic slide‐ring gels carrying sulfoethyl and quaternary ammonium groups on the mobile cross‐links, respectively. The former gel showed intriguing phenomena, including a large degree of swelling of up to 1147, drastic change in its swelling ratio by the presence of electrolyte and bending under a moderate applied electric field (7 V/cm). © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Controllable Electronic Structures and Photoinduced Processes of Bay‐Linked Perylenediimide Dimers and a Ferrocene‐Linked Triad

A series of perylene‐3,4,9,10‐bis(dicarboximide) (PDI) dimers linked through the bay regions was systematically synthesized to examine the electronic structures and photophysical properties in dependence on the distance and orientation between the two PDI units. The spectroscopic and electrochemical measurements suggested that the coupling value of a directly linked PDI dimer (PDI)₂ is much larger than those of para‐ and meta‐phenylene‐bridged PDI dimers p‐(PDI)₂ and m‐(PDI)₂. The width of Davydov splitting was quantitatively evaluated to compare the coupling values between the two PDI units in these dimers by absorption spectroscopy in frozen 2‐methyl‐THF. Excimer formation of PDI dimers induced the strong fluorescence quenching and large red‐shifts. Femtosecond transient absorption revealed a broad absorption derived from an excimer in the range from about 600 nm to the near‐IR region. The rate constants of formation and decay of the excimer are strongly dependent on the coupling values. Time‐resolved measurements on ferrocene‐linked p‐(PDI)₂ revealed a competition between the photoinduced processes of electron transfer and excimer formation in PhCN, which is in sharp contrast with the sole electron‐transfer process in toluene.     

Nagelamide J, a novel dimeric bromopyrrole alkaloid from a sponge Agelas species

A novel dimeric bromopyrrole alkaloid, nagelamide J (1), with antimicrobial activity has been isolated from an Okinawan marine sponge Agelas species, and the structure and stereochemistry were elucidated from spectroscopic data. Nagelamide J (1) is the first bromopyrrole alkaloid possessing a cyclopentane ring fused to an amino imidazole ring.     

Multi-triphenylamine-substituted porphyrin-fullerene conjugates as charge stabilizing "antenna-reaction center" mimics

A new concept of charge stabilization via delocalization of the pi-cation radical species over the donor macrocycle substituents in a relatively simple donor-acceptor bearing multimodular conjugates is reported. The newly synthesized multimodular systems were composed of three covalently linked triphenylamine entities at the meso position of the porphyrin ring and one fulleropyrrolidine at the fourth meso position. The triphenylamine entities were expected to act as energy transferring antenna units and to enhance the electron donating ability of both free-base and zinc(II) porphyrin derivatives of these pentads. Appreciable electronic interactions between the meso-substituted triphenylamine entities and the porphyrin pi-system were observed, and as a consequence, these moieties acted together as an electron-donor while the fullerene moiety acted as an electron-acceptor in the multimodular conjugates. In agreement with the spectral and electrochemical results, the computational studies performed by the DFT B3LYP/3-21G(*) method revealed delocalization of the frontier highest occupied molecular orbital (HOMO) over the triphenylamine entities in addition to the porphyrin macrocycle. Free-energy calculations suggested that the light-induced processes from the singlet excited state of porphyrins are exothermic in the investigated multimodular conjugates. The occurrence of photoinduced charge-separation and charge-recombination processes was confirmed by the combination of time-resolved fluorescence and nanosecond transient absorption spectral measurements. Charge-separated states, on the order of a few microseconds, were observed as a result of the delocalization of the pi-cation radical species over the porphyrin macrocycle and the meso-substituted triphenylamine entities. The present study successfully demonstrates a novel approach of charge-stabilization in donor-acceptor multimodular conjugates.     

Supramolecular triad and pentad composed of zinc-porphyrin(s), oxoporphyrinogen, and fullerene(s): design and electron-transfer studies

By adopting a "covalent-coordinate" bonding approach, novel supramolecular pentad and triad molecules composed of zinc-porphyrin(s), fullerene(s), and oxoporphyrinogen redox-/photoactive entities have been constructed, and also characterized by means of spectral and electrochemical techniques. The geometry and electronic structures of the pentad and the triad were deduced by means of DFT calculations. Free-energy calculations suggested that the photoinduced electron/energy transfer from the zinc-porphyrin (ZnP) singlet-excited state to the imidazole modified fullerene (ImC(60)) acceptor and oxoporphyrinogen (OxP) entities is feasible for both the triad and the pentad. The charge-separation rates (k(CS)) determined from picosecond time-resolved emission studies were higher for pentad (C(60)Im:ZnP)(2)-OxP than for the corresponding triad, C(60)Im:ZnP-OxP. A comparison of the k(CS) values previously reported for the covalently linked bis(zinc-porphyrin)-oxoporphyrinogen triad suggests that employing a fullerene acceptor improves the electron-transfer rates. Nanosecond transient absorption studies provide evidence for the occurrence of electron-transfer processes. Lifetimes of the radical ion pairs (tau(RIP)) are in the range of hundreds of nanoseconds, which indicates that there is charge stabilization in the supramolecular systems.     

Fluorescent tetraruthenated porphyrins embedded in monolithic SiO2 gels by the sol-gel process

In this work silica gels have been prepared by a sol-gel method using tetraethylorthosilicate as gel precursor. The tetraruthenated porphyrins H2(3-TRPyP), Co(3-TRPyP), and H2(4-TRPyP) were incorporated into the systems during gel formation without problems commonly found in the process, such as aggregation. Spectroscopic studies of the resulting silica gels revealed the presence of absorption bands in the range 200-400 nm associated with the transitions of the groups ruthenium-bipyridine, along with the Soret band at the same wavelengths observed in solution. The porphyrins were found to preserve fluorescence emission properties in the range 650-700 nm even after the aging period. Study of the thermal behavior and decomposition kinetics evidenced that the porphyrin H2(4-TRPyP) is the least stable of the group and that all compounds decompose according to first-order kinetics.     

Synthesis, structures, and properties of meso-phosphorylporphyrins: self-organization through P-oxo-zinc coordination

The synthesis, structures, and optical and electrochemical properties of meso-phosphorylporphyrins are described. The copper-catalyzed carbon-phosphorus cross-coupling reaction of a meso-iodoporphyrin with di-n-butyl phosphite and diphenylphosphane oxide has proved to be an efficient and general method for the synthesis of meso-phosphorylporphyrins. Zinc phosphorylporphyrins thus obtained readily undergo self-organization through P-oxo-Zn coordination to form noncovalently linked, cofacial porphyrin dimers or linear oligomers, which have been characterized by spectroscopic methods and X-ray crystallographic analyses. In toluene, CH(2)Cl(2), and CHCl(3), the zinc phosphorylporphyrins exist mostly as dimers or monomers, depending on their concentrations, the temperature, and the presence of additives. The self-association constants for dimerization in toluene have been determined by UV/Vis absorption titration measurements. The meso-diphenylphosphorylporphyrin dimer displays excitonic coupling of the Soret band with a splitting energy of 940 cm(-1). Fluorescence lifetimes of the zinc phosphorylporphyrins have been found to be affected only slightly by the concentration of the solution, and by the addition of triphenylphosphane oxide, suggesting that the effect of dimerization on their photodynamics in the S(1) state is negligible. On the other hand, the effect of dimerization is clearly reflected in their electrochemical oxidation processes, as the initially produced radical cations are efficiently delocalized over the two porphyrin rings. These findings demonstrate the potential utility of meso-phosphorylporphyrins as new models for the special pair in photosynthesis and as new building blocks for porphyrin-based supramolecular materials.     

Enantioselective total synthesis of (+)-ottelione A, (-)-ottelione B, (+)-3-epi-ottelione A and preliminary evaluation of their antitumor activity

Enantioselective total synthesis of (+)-ottelione A (1) and (-)-ottelione B (2), novel and potent antitumor agents from a freshwater plant, and (+)-3-epi-ottelione A (3), the earlier proposed stereostructure of 1, was efficiently achieved starting from the known tricyclic compound 10. The synthesis involved the following key steps: i) coupling reactions of aldehydes 8 and 9 with the aromatic portion 7 (8+7-->15 and 9+7-->27), ii) base-induced hemiacetal-opening/epimerization reactions of the cyclic hemiacetals 6 and 27 (6-->17 and 27 a-->26 a), and iii) Corey-Winter's reductive olefination of the cyclic thiocarbonates 21 and 36 (21-->22 and 36-->37). The present total synthesis fully established the absolute configuration of these natural products. The cell growth inhibition profile, COMPARE analysis, and tubulin inhibitory assay of (+)-3-epi-ottelione A (3) and its O-acetyl derivative 24 demonstrated that these unnatural substances could be prominent lead compounds for the development of anticancer agents with a novel mode of action.