Effect of DNA flanking sequence on charge transport in short DNA duplexes

Several factors can influence charge transport (CT)-mediated DNA, such as sequence, distance, base stacking, base pair mismatch, conformation, tether length, etc. However, the DNA context effect or how flanking sequences influence redox active drugs in the DNA CT reaction and later in DNA enzymatic repair and synthesis is still not well understood. The set of seven DNA molecules in this study have been characterized well for the study of flanking sequence effects. These DNA duplexes are formed from self-complementary strands and contain the common central four-base sequence 5'-A-G-C-T-3', flanked on both sides by either (AT)(n) or (AA)(n) (n = 2, 3, or 4) or AA(AT)(2). UV-vis, fluorescence, UV melting, circular dichroism, and cyclic voltammetry experiments were used to study the flanking sequence effect on CT-mediated DNA by using daunomycin or adriamycin cross-linked with these seven DNA molecules. Our results showed that charge transport was related to the flanking sequence, DNA melting free energy, and ionic strength. For (AA)(n) or (AT)(n) species of the same length, (AA)(n) series were more stable and more efficient CT was observed through the (AA)(n) series. The same trend was observed for (AA)(n) and (AT)(n) series at different ionic strengths, further supporting the idea that flanking sequence can result in different base stacking and modulate charge transport through these seven DNA molecules.

Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

Tentative study of the coding sequences without 3-base periodicity

Fourier spectra of 120 short coding sequences (<1 200 bp) show that not all coding sequences are characterized by 3-base periodicity. Statistical analysis suggests that whether a coding sequence has 3-base periodicity may be related to the composition and distribution of bases, the usage and the order of the amino acids of the encoded protein as well as the synonymous codon usage. Generally, the content of A+U is higher than that of G+C in non-period-3 sequences, inversely in period-3 sequences. In the three codon positions, the base distribution in the non-periodic-3 sequences is more uniform than in the periodic-3 sequences. The usage biases of the amino acids and the codons in non-period-3 sequences are weaker than that in period-3 sequences. All of these phenomena should be considered sufficiently in predicting the genes and exons of DNA sequences by Fourier analysis method.

Characterization of complete genome sequence of the spring viremia of carp virus isolated from common carp (Cyprinus carpio) in China

The complete genome of spring viraemia of carp virus (SVCV) strain A-1 isolated from cultured common carp (Cyprinus carpio) in China was sequenced and characterized. Reverse transcription-polymerase chain reaction (RT-PCR) derived clones were constructed and the DNA was sequenced. It showed that the entire genome of SVCV A-1 consists of 11,100 nucleotide base pairs, the predicted size of the viral RNA of rhabdoviruses. However, the additional insertions in bp 4633-4676 and bp 4684-4724 of SVCV A-1 were different from the other two published SVCV complete genomes. Five open reading frames (ORFs) of SVCV A-1 were identified and further confirmed by RT-PCR and DNA sequencing of their respective RT-PCR products. The 5 structural proteins encoded by the viral RNA were ordered 3'-N-P-M-G-L-5'. This is the first report of a complete genome sequence of SVCV isolated from cultured carp in China. Phylogenetic analysis indicates that SVCV A-1 is closely related to the members of the genus Vesiculovirus, family Rhabdoviridae.

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp - Cyprinus carpio haematopterus, Yuanjiang River wild common carp Cyprinus carpio rubrofuscus and Volga River wild common carp - Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus.

Complete genome sequence of lymphocystis disease virus isolated from China

Lymphocystis diseases in fish throughout the world have been extensively described. Here we report the complete genome sequence of lymphocystis disease virus isolated in China (LCDV-C), an LCDV isolated from cultured flounder (Paralichthys olivaceus) with lymphocystis disease in China. The LCDV-C genome is 186,250 bp, with a base composition of 27.25% G+C. Computer-assisted analysis revealed 240 potential open reading frames (ORFs) and 176 nonoverlapping putative viral genes, which encode polypeptides ranging from 40 to 1,193 amino acids. The percent coding density is 67%, and the average length of each ORF is 702 bp. A search of the GenBank database using the 176 individual putative genes revealed 103 homologues to the corresponding ORFs of LCDV-1 and 73 potential genes that were not found in LCDV-1 and other iridoviruses. Among the 73 genes, there are 8 genes that contain conserved domains of cellular genes and 65 novel genes that do not show any significant homology with the sequences in public databases. Although a certain extent of similarity between putative gene products of LCDV-C and corresponding proteins of LCDV-1 was revealed, no colinearity was detected when their ORF arrangements and coding strategies were compared to each other, suggesting that a high degree of genetic rearrangements between them has occurred. And a large number of tandem and overlapping repeated sequences were observed in the LCDV-C genome. The deduced amino acid sequence of the major capsid protein (MCP) presents the highest identity to those of LCDV-1 and other iridoviruses among the LCDV-C gene products. Furthermore, a phylogenetic tree was constructed based on the multiple alignments of nine MCP amino acid sequences. Interestingly, LCDV-C and LCDV-1 were clustered together, but their amino acid identity is much less than that in other clusters. The unexpected levels of divergence between their genomes in size, gene organization, and gene product identity suggest that LCDV-C and LCDV-1 shouldn't belong to a same species and that LCDV-C should be considered a species different from LCDV-1.

Copper phthalocyanine based hybrid p-type permeable-base transistor in vertical architecture

We demonstrate the production of copper phthalocyanine (CuPc) based p-type hybrid permeable-base transistors, which operate at low voltages having high common-base current gains. These transistors are prepared by evaporating a thin metal layer (Ag or Al) that acts as base on top of a Si substrate that acts as collector. In the sequence CuPc and Au are thermally sublimated to produce the emitter, constituting a quite simple device production procedure with the additional advantage of allowing higher integration due to its vertical architecture.

SYNTHESIS OF A NEW CHIRAL LIQUID-CRYSTAL WITH SCHIFF-BASE GROUP AND INVESTIGATION OF TEMPERATURE-DEPENDING FTIR SPECTRA

A new chiral liquid crystal with Schiff base group has been prepared, The structure of liquid crystal was confirmed by elementary analyses and H-1 NMR. Its phase transition was investigated by polarized optical microscope, DSC and temperature-depending FTIR spectra. The results showed that the chiral Schiff base showed monotropic phases behavior in certain temperature range, the phase sequence is I-N-*-S-B-S-G-K on the cooling sequence.

Characters of variation of LURR during the earthquake sequence of Xinjiang

The theory of the loading/unloading response ratio (LURR) was applied to the Jiashi earthquake sequence which occurred at the beginning of 1997 in Xinjiang, and found that, before the earthquakes with relatively high magnitudes In the sequence, the ratio showed anomalies of high values. That is to say, the LURR theory can be applied to the short-term earthquake prediction in some cases, especially in the early period after a strong earthquake, such as the forecasts for some strong earthquakes in the Jiashi sequence.

Theoretical analysis for mechanical erosion of carbon-base materials in ablation

This article derives and provides a theoretical analysis for the mechanical erosion of carbon-base materials in ablation. The theory of mechanical erosion based on a nondimensional critical roughness parameter is proposed, The important parameters in this analytical method are independent of the test, The analysis accounts for the heating, pressure, and shear forces acting on material particles exposed to the boundary-layer flow. For the validity of a theoretical analytical method a computational example is given. The theoretical results agree fairly with the experimental data.

Structures on sliding base subject to horizontal and vertical motions

In this paper particular investigation is directed towards the combined effects of horizontal and vertical motions of real earthquakes to structures resting on sliding base. A simplified method is presented to treat the nonlinear effects of time dependent frictional force of the sliding base as a function of the vertical reaction produced by the foundation. As an example, the El Centro 1940 earthquake record is used on a structural model to show the structural responses due to a sliding base with different frictional and stiffness characteristics. The study shows that vertical ground motion does affect both the superstructure response and the base sliding displacement. Nevertheless, the sliding base isolator is shown to be effective for the reduction of seismic response of a superstructure.

Asymmetry of the photoionization rate of H atoms by a sequence of one-cycle laser pulses

Using an unperturbed scattering theory, the characteristics of H atom photoionization are studied respectively by a linearly- and by a circularly- polarized one-cycle laser pulse sequence. The asymmetry for photoelectrons in two directions opposite to each other is investigated. It is found that the asymmetry degree varies with the carrier-envelope (CE) phase, laser intensity, as well as the kinetic energy of photoelectrons. For the linear polarization, the maximal ionization rate varies with the CE phase, and the asymmetry degree varies with the CE phase in a sine-like pattern. For the circular polarization, the maximal ionization rate keeps constant for various CE phases, but the variation of asymmetry degree is still in a sine-like pattern.

In situ surface topography measurement method of granite base in scanning wafer stage with laser interferometer

Topography of a granite surface has an effect on the vertical positioning of a wafer stage in a lithographic tool, when the wafer stage moves on the granite. The inaccurate measurement of the topography results in a bad leveling and focusing performance. In this paper, an in situ method to measure the topography of a granite surface with high accuracy is present. In this method, a high-order polynomial is set up to express the topography of the granite surface. Two double-frequency laser interferometers are used to measure the tilts of the wafer stage in the X- and Y-directions. From the sampling tilts information, the coefficients of the high-order polynomial can be obtained by a special algorithm. Experiment results shows that the measurement reproducibility of the method is better than 10 nm. (c) 2006 Elsevier GmbH. All rights reserved.

Adaptive image sequence coding based on global and local compensability analysis

Our study of a novel technique for adaptive image sequence coding is reported. The number of reference frames and the intervals between them are adjusted to improve the temporal compensability of the input video. The bits are distributed more efficiently on different frame types according to temporal and spatial complexity of the image scene. Experimental results show that this dynamic group-of-picture (GOP) structure coding scheme is not only feasible but also better than the conventional fixed GOP method in terms of perceptual quality and SNR. (C) 1996 Society of Photo-Optical Instrumentation Engineers.