Non-empirical calculations of NMR indirect carbon-carbon coupling constants. Part 10--carbocages

A comprehensive theoretical study of nine classical caged polycycloalkanes (tetrahedrane, prismane, homoprismane, quadricyclane, cubane, pentaprismane, hexaprismane, adamantane and diamantane) was carried out with special focus on the structural behavior of their J(C,C) values calculated at the SOPPA level. The structural behavior of J(C,C) in small carbocages is dominated by steric strain whereas in medium-sized polycycloalkanes the J(C,C) values show no marked peculiarities and follow several well-defined structural trends typical of other alicyclic compounds.     

Hybrid Genetic Algorithm for DNA Sequencing with Errors

In the paper, a new hybrid genetic algorithm solving the DNA sequencing problem with negative and positive errors is presented. The algorithm has as its input a set of oligonucleotides coming from a hybridization experiment. The aim is to reconstruct an original DNA sequence of a known length on the basis of this set. No additional information about the oligonucleotides nor about the errors is assumed. Despite that, the algorithm returns for computationally hard instances surprisingly good results, of a very high similarity to original sequences.     

Near ab initio quality molecular electrostatic potential maps using hybridization displacement charges at PM3 level and effects of geometrical changes in amino groups

Charge distributions, dipole moments, and molecular electrostatic potentials (MEP) around several molecules consisting of carbon, nitrogen, oxygen, fluorine, sulfur, and chlorine atoms were studied using the PM3 semiempirical method and the results compared with those obtained using ab initio calculations at the RHF/6‐31G** level. Thus it is shown that relative MEP values near different atoms can be obtained using hybridization displacement charges (HDC) obtained by employing PM3 density matrices that usually agree quite satisfactorily with the ab initio ones. Further, positions of ab initio MEP minima are correctly located and the corresponding relative MEP values usually correctly predicted using the PM3(HDC) charges distributed continuously in three dimensions according to the forms of squares of valence s atomic orbitals. The necessary parameters for HDC calculations using the PM3 method were optimized. It is shown how within the frameworks of both PM3 and AM1 methods the π electrons or lone pairs associated with amino group nitrogen atoms and ring atoms can be satisfactorily treated in different situations. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 299–312, 2001     

基于金纳米粒子的QCM实时检测DNA错配的研究

利用石英晶体微天平（QCM）技术,用双硫醇分子作为连接剂,将金纳米粒子固定于金电极表面,以人类p53基因片断为DNA探针,研究了其在QCM金电极表面的固定、杂交和错配,重点探讨了金纳米粒子修饰的DNA错配碱基个数和错配位点对杂交的影响。在实验条件下,金纳米粒子在QCM金电极表面的修饰使其灵敏度得到了明显提高;而且,错配碱基个数和错配碱基位点的差异都对杂交产生了不同程度的影响。     

Gene Expression Profile of Prostate Cancer Patients by Chemiluminescent Analysis

Abstract

The heterogeneous and multifactorial nature of prostate cancer that generates differential gene expression patterns in tumor cells leads us to investigate the molecular mRNA profiling of 14 genes through streptavidin-alkaline phosphatase–labeled RNA probes from tissue samples with prostate cancer and benign prostatic hyperplasia. Hybridizations were performed using cDNA amplification for each gene spotted onto positively charged nylon membranes and densitometry readings. The constitutive gene GAPDH was used to normalize the data. The methods developed in this study may be applicable to the prostate cancer diagnosis using AR, CEACAM-1, DD3 (also called PCA3), OPN-1, and PSMA significant differential expression.     

A high‐resolution hybrid scheme for hyperbolic conservation laws

A new hybrid scheme is proposed, which combines the improved third‐order weighted essentially non‐oscillatory (WENO) scheme presented in this paper with a fourth‐order central scheme by a novel switch. Two major steps have been gone through for the construction of a high‐performance and stable hybrid scheme. Firstly, to enhance the WENO part of the hybrid scheme, a new reference smoothness indicator has been devised, which, combined with the nonlinear weighting procedure of WENO‐Z, can drive the third‐order WENO toward the optimal linear scheme faster. Secondly, to improve the hybridization with the central scheme, a hyperbolic tangent hybridization switch and its efficient polynomial counterpart are devised, with which we are able to fix the threshold value introduced by the hybridization. The new hybrid scheme is thus formulated, and a set of benchmark problems have been tested to verify the performance enhancement. Numerical results demonstrate that the new hybrid scheme achieves excellent performance in resolving complex flow features, even compared with the fifth‐order classical WENO scheme and WENO‐Z scheme. Copyright © 2015 John Wiley & Sons, Ltd.     

Spiropyran Photoswitches in the Context of DNA: Synthesis and Photochromic Properties

A new design is presented for the incorporation of spiropyran photoswitches into nucleic acids by oligonucleotide solid phase synthesis. This design enables interaction of the 6‐nitrospirobenzopyran (NitroBIPS) photoswitch with the adjacent nucleobases and leaves the photochemical properties of NitroBIPS intact. UV/Vis spectroscopy and HPLC revealed that NitroBIPS incorporated into DNA consists of up to 40 % merocyanine in its thermal equilibrium and undergoes reversible switching between the photoisomeric spiropyran (SP) and merocyanin (MC) state by alternating excitation using visible light or heat for at least fifteen switching cycles. Exchanging the chromene part of NitroBIPS on the DNA level gives access to differently substituted spiropyran derivatives allowing the screening for spiropyrans with suitable properties in a straightforward manner. Thus, by incorporating the highly hydrolysis‐stable pyrido‐spiropyran derivative PyBIPS pure light‐triggered reversible switching of a spiropyran in DNA has been realized for the first time. Therefore, this design represents a new useful platform for investigating the photochromic behavior of different spiropyran photoswitches in a nucleic acid environment and for using spiropyrans to induce light‐ or heat‐triggered changes in conformations or in fluorescence quenching properties of oligonucleotides.     

Charge transfer effects on the Fermi surface of Ba0.5K0.5Fe2As2

Ab‐initio calculations within density functional theory are performed to obtain a more systematic understanding of the electronic structure of iron pnictides. As a prototypical compound we study Ba_0.5K_0.5Fe₂As₂ and analyze the changes of its electronic structure when the interaction between the Fe₂As₂ layers and their surrounding is modified. We find strong effects on the density of states near the Fermi energy as well as the Fermi surface. The role of the electron donor atoms in iron pnictides thus cannot be understood in a rigid band picture. Instead, the bonding within the Fe₂As₂ layers reacts to a modified charge transfer from the donor atoms by adapting the intra‐layer Fe‐As hybridization and charge transfer in order to maintain an As^3‐ valence state.     

Ionic Liquid Modified Single‐use Electrode Developed for Voltammetric Detection of miRNA‐34a and its Application to Real Samples

The ionic liquid (IL) modified chemically activated (CA) pencil graphite electrodes (PGEs) were developed for label‐free voltammetric detection of miRNA‐34a, and implemented to the real samples. Firstly, the electrochemical characterization of unmodified PGE, CA‐PGE, IL‐PGE and IL‐CA‐PGE was performed by cyclic voltammetry (CV) as well as their DNA binding capacity was studied by electrochemical impedance spectroscopy (EIS) technique. The microscopic characterization of the surface of each electrodes was investigated by scanning electron microscopy (SEM). Differential pulse voltammetry (DPV) technique was used for measuring the oxidation signal of guanine in order to perform a label‐free voltammetric monitoring of a full‐match hybridization specific to miRNA‐34a. The selectivity of biosensor was tested against to miRNA‐155, miRNA‐660 as well as to the mismatch sequence of miRNA‐34a. The further selectivity of this proposed biosensor was studied in the mixture of samples containing miRNA‐34a with other miRNAs (1 : 1). The voltammetric detection of miRNA‐34a was also explored in the artificial serum medium as fetal bovine serum (FBS) and also in total RNA samples isolated from HUH‐7 human hepatocellular carcinoma cell line.