Circumventing air bubbles in microfluidic systems and quantitative continuous-flow PCR applications

Polymerase chain reaction (PCR) is an essential part of research based on genomics or cell analysis. The development of a microfluidic device that would be suitable for high-temperature-based reactions therefore becomes an important contribution towards the integration of micro-total analysis systems (μTAS). However, problems associated with the generation of air bubbles in the microchannels before the introduction of the assay liquid, which we call the “initial start-up” in this study, made the flow irregular and unstable. In this report, we have tried to address these problems by adapting a novel liquid-flow method for high-temperature-based reactions. A PDMS-based microfluidic device was fabricated by soft-lithography techniques and placed on a cartridge heater. The generation of the air bubbles was prevented by introducing the fluorinated oil, an inert and highly viscous liquid, as the cap just before the introduction of the sample solutions into the microchannels. The technique was applied for continuous-flow PCR, which could perform PCR on-chip in a microfluidic system. For the evaluation of practical accuracy, plasmid DNA that serves as a reference molecule for the quantification of genetically modified (GM) maize was used as the template DNA for continuous-flow PCR. After PCR, the products were collected in a vial and analyzed by gel electrophoresis to confirm the accuracy of the results. Additionally, quantitative continuous-flow PCR was performed using TaqMan technology on our PCR device. A laser detection system was also used for the quantitative PCR method. We observed a linear relationship between the threshold cycle (Ct) and the initial DNA concentration. These results showed that it would be possible to quantify the initial copies of the template DNA on our microfluidic device. Accurate quantitative DNA analysis in microfluidic systems is required for the integration of PCR with μTAS, thus we anticipate that our device would have promising potential for applications in a wide range of research.     

Stereoselective Synthesis of the Proposed C79–C104 Fragment of Symbiodinolide

Stereoselective and streamlined synthesis of the proposed C79–C104 fragment 2 of symbiodinolide ( 1 ), a polyol marine natural product with a molecular weight of 2860, was achieved. In the synthetic route, the proposed C79–C104 fragment 2 was synthesized by utilizing a Julia–Kocienski olefination and subsequent Sharpless asymmetric dihydroxylation as key transformations in a convergent manner. Detailed comparison of the ¹³C NMR chemical shifts between the natural product and the synthetic C79–C104 fragment 2 revealed that the stereostructure at the C91–C99 carbon chain moiety of symbiodinolide ( 1 ) should be reinvestigated.     

Formal total synthesis of enigmazole A

A stereoselective formal total synthesis of enigmazole A, a marine macrolide isolated from Cinachyrella enigmatica, is described. Lewis acid mediated intramolecular allylation of an α-acetoxy ether, prepared from alcohol and carboxylic acid fragments was carried out to construct the methylene THP ring with high stereoselectivity. The late-stage macrolactonization of the corresponding seco-acid provided a known synthetic intermediate of enigmazole A.     

Stable meso‐Aryl β‐Alkyl Hybrid Sapphyrin with a Warped π‐Conjugation Circuit and Neo‐Confused Sapphyrin–Silver(I) Complex

A meso‐aryl and β‐alkyl substituted sapphyrin and its rhodium(I) and silver complexes were synthesized. This sapphyrin was so stable that the non‐inverted and warped structure could be analyzed by X‐ray crystallography even in its neutral state. Its bis‐rhodium(I) complex has a more planar structure than the sapphyrin with enhanced aromaticity over the conjugation circuit. On the other hand, silver metalation of the sapphyrin caused a marked core rearrangement into a neo‐confused sapphyrin derivative with a C(α)?N bond and a twisted macrocycle.     

Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation

Molecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water-phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between alpha-helix and beta-sheet structures was significantly improved by the modification of charge parameters.     

Force field parameters for rotation around chi torsion axis in nucleic acids

To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.     

Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

Hamiltonian cycles on random lattices of arbitrary genus

A Hamiltonian cycle of a graph is a closed path that visits every vertex once and only once. It has been difficult to count the number of Hamiltonian cycles on regular lattices with periodic boundary conditions, e.g. lattices on a torus, due to the presence of winding modes. In this paper, the exact number of Hamiltonian cycles on a random trivalent fat graph drawn faithfully on a torus is obtained. This result is further extended to the case of random graphs drawn on surfaces of an arbitrary genus. The conformational exponent y is found to depend on the genus linearly.