High-Density Nucleoside Analog Probe Arrays for Enhanced Hybridization

Abstract

DNA probe arrays were synthesized with analogs of 2,6-diaminopurine and 2′-O-methyl-thymidine in place of A and T. AT-rich GeneChip® test arrays containing 14-mer or 20-mer analog probes improved hybridization to fluorescently-labeled RNA sequences under stringent conditions.     

Photolithographic synthesis of high-density oligonucleotide probe arrays

High-density DNA probe arrays provide a massively parallel approach to nucleic acid sequence analysis that is transforming gene-based biomedical research and diagnostics. Light-directed combinatorial oligonucleotide synthesis has enabled the large-scale production of GeneChip probe arrays which contain several hundred of thousand oligonucleotide sequences on glass "chips" about one cm2 in size. Due to their very high information content, GeneChip probe arrays are finding widespread use in the hybridization-based detection and analysis of mutations and polymorphisms ("genotyping"), and in a wide range of gene expression studies. The manufacturing process integrates solid-phase photochemical oligonucleotide synthesis with lithographic techniques adapted from the microelectronics industry. The present-generation methodology employs MeNPOC photo-activatable nucleoside monomers with proximity photolithography, and is currently capable of printing individual 10 microns 2 probe features at a density of 10(6) probes/cm2.     

Plasma and ion beam injection into an FRC

Experiments on the transverse injection of intense (5–20 A/cm²), wide cross-section (10-cm), neutralized, ～100-eV H⁺ plasma and 100-keV H⁺ ion beams into a preformed B-field reversed configuration (FRC) are described. The FRC background plasma temperature was ～5 eV with densities of ～10¹³ cm^?3. In contrast to earlier experiments, the background plasma was generated by separate plasma gun arrays. For the startup of the FRC, a betatron-type “slow” coaxial source was used. Injection of the plasma beam into the preformed FRC resulted in a 30–40% increase of the FRC lifetime and the amplitude of the reversed magnetic field. As for the ion beam injection experiment into the preformed FRC, there was evidence of beam capture within the configuration.     

Rapid detection of “Candidatus Phytoplasma mali” by recombinase polymerase amplification assays

Isothermal recombinase polymerase amplification (RPA) assays for the specific detection of “Candidatus Phytoplasma mali (Ca. P. mali),” the causal agent of apple proliferation, were developed. The assays amplify a fragment of the imp gene and amplimers were detected either by fluorescence in real‐time mode (TwistAmp^®exo assay) using a fluorophore‐labelled probe or by direct visualization employing a lateral flow device (TwistAmp^®nfo assay/Milenia^®HybriDetect). The RPA assays specifically amplified DNA from “Ca. P. mali” strains, and cross‐reactivity with other phytoplasmas or plant DNA was not observed. The limit of detection was determined with a cloned imp standard, and positive results were obtained down to 10 copies with both RPA assay formats. In comparison with a TaqMan real‐time PCR assay based on the same target gene, the RPA assays were equally sensitive, but results were obtained faster. Simplified nucleic acid extraction procedures from plant tissue with Tris‐ and CTAB‐based buffers revealed that crude Tris–DNA extracts were a suitable source for RPA tests while larger concentrations of CTAB were inhibitory. This is the first report of RPA‐based assays for the detection of “Ca. P. mali”. The assays are suitable for high‐throughput screening of plant material and point‐of‐care diagnostic and can be potentially combined with a simplified DNA extraction procedure.     

Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis

Background

High-density oligonucleotide arrays have become a valuable tool for high-throughput gene expression profiling. Increasing the array information density and improving the analysis algorithms are two important computational research topics.

Results

A new algorithm, Match-Only Integral Distribution (MOID), was developed to analyze high-density oligonucleotide arrays. Using known data from both spiking experiments and no-change experiments performed with Affymetrix GeneChip^® arrays, MOID and the Affymetrix algorithm implemented in Microarray Suite 4.0 (MAS4) were compared. While MOID gave similar performance to MAS4 in the spiking experiments, better performance was observed in the no-change experiments. MOID also provides a set of alternative statistical analysis tools to MAS4. There are two main features that distinguish MOID from MAS4. First, MOID uses continuous P values for the likelihood of gene presence, while MAS4 resorts to discrete absolute calls. Secondly, MOID uses heuristic confidence intervals for both gene expression levels and fold change values, while MAS4 categorizes the significance of gene expression level changes into discrete fold change calls.

Conclusions

The results show that by using MOID, Affymetrix GeneChip^® arrays may need as little as ten probes per gene without compromising analysis accuracy.     

Nucleoside 3′-O-(2-Oxo-“Spiro”-4.4-Pentamethylene-1.3.2-Oxathiaphospholane)S: Monomers For Stereocontrolled Synthesis Of Oligo(Nucleoside Phosphorothioate/Phosphate)S

Abstract

Attempts at synthesis of “chimeric” oligonucleotide constructs (PO/PS-Oligos) possessing phosphate and P-stereodefined phosphorothioate internucleotide linkages via combined phosphoramidite/oxathiaphospholane methods were unsuccessful. Therefore, novel monomers for oxathiaphospholane method, namely 5′-O-DMT-deoxyribonucleoside 3′-O(2-oxo-.spiro-4.4-pentamethylene-1.3.2-oxathiaphospholane)s, were prepared and used together with their diastereomerically pure 2-thio analogues for the stereocontrolled synthesis of “chimeric” oligonucleotide constructs (PO/PS-Oligos).     

The “Midas Touch” Transformation of TiO2 Nanowire Arrays during Visible Light Photoelectrochemical Performance by Carbon/Nitrogen Coimplantation

Titanium dioxide is a promising photoanode material for water oxidation, but it is substantially limited by its poor efficiency in the visible light range. Herein, an innovative carbon/nitrogen coimplantation method is utilized to realize the “Midas touch” transformation of TiO₂ nanowire (NW) arrays for photoelectrochemical (PEC) water splitting in visible light. These modified golden–yellow rutile TiO₂ NW arrays (C/N‐TiO₂) exhibit remarkably enhanced absorption in visible light regions and more efficient charge separation and transfer. As a result, the photocurrent density of carbon/nitrogen co‐implanted TiO₂ under visible light (>420 nm) can reach 0.76 mA cm^?2, which far exceeds the value of 3 µA cm^?2 seen for pristine TiO₂ nanowire arrays at 0.8 V versus Ag/AgCl. An incident photon to electron conversion efficiency of ≈14.8% is achieved at 450 nm on C/N‐TiO₂ without any other cocatalysts. The ion implantation doping approach, combined with codoping strategies, is proved to be an effective strategy for enhancing the photoelectrochemical conversion and can enable further improvement of the PEC water‐splitting performance of many other semiconductor photoelectrodes.     

Improved Procedure for the Reduction of N - 1 Content in Synthetic Oligonucleotides

Abstract

By incorporating a “capping step” at the start of an oligonucleotide synthesis (“pre-cap”) and following a “SUP” work-up protocol with ammonium hydroxide, an overall improvement is observed in the quality of oligonucleotides synthesized on a large scale on controlled pore glass support (CPG). Rationalization of these results is provided.     

3D Vertically Aligned Li Metal Anodes with Ultrahigh Cycling Currents and Capacities of 10 mA cm−2/20 mAh cm−2 Realized by Selective Nucleation within Microchannel Walls

Although metallic lithium is regarded as the “Holy Grail” for next‐generation rechargeable batteries due to its high theoretical capacity and low overpotential, the uncontrollable Li dendrite growth, especially under high current densities and deep plating/striping, has inhibited its practical application. Herein, a 3D‐printed, vertically aligned Li anode (3DP‐VALi) is shown to efficiently guide Li deposition via a “nucleation within microchannel walls” process, enabling a high‐performance, dendrite‐free Li anode. Moreover, the microchannels within the microwalls are beneficial for promoting fast Li⁺ diffusion, supplying large space for the accommodation of Li during the plating/stripping process. The high‐surface‐area 3D anode design enables high operating current densities and high areal capacities. As a result, the Li–Li symmetric cells using 3DP‐VALi demonstrate excellent electrochemical performances as high as 10 mA cm^?2/10 mAh cm^?2 for 1500 h and 5 mA cm^?2/20 mAh cm^?2 for 400 h, respectively. Additionally, the Li–S and Li–LiFePO₄ cells using 3DP‐VALi anodes present excellent cycling stability up to 250 and 800 cycles at a rate of 1 C, respectively. It is believed that these new findings could open a new window for dendrite‐free metal anode design and pave the way toward energy storage devices with high energy/power density.     

Prokaryotic RNA preparation methods useful for high density array analysis: comparison of two approaches

High density oligonucleotide arrays have been used extensively for expression studies of eukaryotic organisms. We have designed a prokaryotic high density oligonucleotide array using the complete Escherichia coli genome sequence to monitor expression levels of all genes and intergenic regions in the genome. Because previously described methods for preparing labeled target nucleic acids are not useful for prokaryotic cell analysis using such arrays, a mRNA enrichment and direct labeling protocol was developed together with a cDNA synthesis protocol. The reproducibility of each labeling method was determined using high density oligonucleotide probe arrays as a read-out methodology and the expression results from direct labeling were compared to the expression results from the cDNA synthesis. About 50% of all annotated E.coli open reading frames are observed to be transcribed, as measured by both protocols, when the cells were grown in rich LB medium. Each labeling method individually showed a high degree of concordance in replica experiments (95 and 99%, respectively), but when each sample preparation method was compared to the other, ~32% of the genes observed to be expressed were discordant. However, both labeling methods can detect the same relative gene expression changes when RNA from IPTG-induced cells was labeled and compared to RNA from uninduced E.coli cells.     

Variations spectroscopiques induites par illumination et par action chimique observées à—196°C dans la chlorophylle a de Porphyridium

Spectroscopic Changes in the Chlorophyll a of Porphyridium Induced by Illumination and Chemical Action and Observed at ?196°C. Photo-oxidation of P700 by 708 nm light can take place under weak intensity (10^?6 W × cm^?2) when the medium is frozen. Spectral characteristics of “700 nm” and “690 nm” variations are accurately measured. The amplitude of the photoinduced changes of absorption are similar to those induced by chemical action. In the case of Porphyridium, an apparent increase of the extinction power of P700 at ?196°C is observed. This fact seems to be due to a diminution of the bandwith of the neighbouring pigments. Irradiation with red light (685 nm), of a relatively high intensity (10^?2 W × cm^?2), in the presence of oxygen at ?196°C, induces a slight shift (0.5 nm) of the red absorption band maximum towards longer wavelengths. This change is similar to the one promoted by ferricyanide in the dark. The origin and the functional significance of the phenomenon is discussed.     

Organization and Control of Microtubule Pattern in Centrohelidan Heliozoa*†

SYNOPSIS. Comparative studies of axopodial microtubule pattern in 10 different centrohelidan Heliozoa belonging to the genera Acanthocystis, Raphidiophrys and Heterophrys suggest that 2 basic principles govern pattern formation in centrohelidan Heliozoa. While the larger “open” arrays with unspecified number of microtubules, e.g. in A. aculeata and R. ambigua, may result from self-linkage of additional microtubules around centroplast-nucleated “starter microtubules,” the smaller “closed” arrays with specified microtubule number, e.g. in A. pectinata and H. marina, favor a template-driven linkage mechanism. The centroplast is a highly complex microtubule organizing center involved in the control of orientation, number, and diameter of the axonemes. Its shell may serve as a surface upon which the microtubule nucleating sites assemble, but how the precise positioning of these sites occurs is still open to debate. Some of the unsolved problems of microtubule pattern formation may be explained by the “linker nucleation hypothesis” which is an extension of the “gradion hypothesis” by Roth et al. It is shown how both the formation of closed arrays and the balanced lateral growth of open arrays may result from linker-induced microtubule nucleation.     

Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS)

A novel label-free biosensor concept based on surface plasmon-enhanced diffraction by micro- patterned interfaces was applied to the study of hybridization reactions of target DNA oligonucleotides (15mers and 75mers) from solution to probe DNA oligonucleotides attached via streptavidin to the sensor surface. The self-referencing and quadratic signal amplification mechanism of the sensor allowed highly sensitive detection of the hybridization process. Association and dissociation processes of DNA targets could be recorded in real time and used for the quantification of their binding affinities, which differ considerably with a single base pair mismatch. An equilibrium titration approach was also applied in order to obtain the binding affinities for 15mer targets, yielding similar affinity values. The hybridization efficiencies were found to be higher for the 15mers than for the 75mers, although the latter contained the same recognition sequences. The hybridization efficiency was shown to depend on the probe density and reached nearly 100% for the 15mer fully complementary targets at a probe density of ~1.2 × 10¹² molecules/cm². Using the assay as an end-point determination method, the lowest detectable coverage of a 15mer oligonucleotide was at least ~1.1 × 10¹¹ molecules/cm². The diffraction sensing concept offers a completely novel way to integrate a reference channel in large-scale, label-free screening applications, to improve the stability and to enhance the sensitivity of microarray read-out systems.     

Polypyrimidine segments in drosophila melanogaster DNA: I. Detection of a cryptic satellite containing polypyrimidine/polypurine DNA

Very long runs of pyrimidine nucleotides (polypyrimidines), previously detected in DNA from Drosophila melanogaster, have now been localized to a “cryptic” satellite. These polypyrimidines have an average length of 750 nucleotides and account for about 3% of the thymine residues in total DNA. The buoyant density of the DNA component which contains the polypyrimidines was detected by centrifuging native DNA to equilibrium in a CsCI gradient, and then assaying each fraction for its content of polypyrimidines. A peak was detected at a density of about 1.707 gm/cm³, distinctly heavier than the main band of DNA (1.702 gm/cm³). The buoyant density of polypyrimidine-containing molecules was little affected by differences in the molecular weight of the starting DNA in the range 10⁵-10⁷ daltons (single-stranded). Thus polypyrimidines (and their complementary polypurines) appear to form all or part of a “cryptic” satellite.Polypyrimidines have been isolated and characterized with respect to composition and buoyant density. Direct nucleoside analysis of unlabeled material indicated 34.5% deoxycytidine, 65.5% thymidine. Their banding position in neutral and alkaline CsCI gradients was consistent with a single-stranded DNA polymer of this composition.     

Supplementation of 2nd break mushroom compost with isoleucine, leucine, valine, phenylalanine, Fermenten® and SoyPlus®

Three mushroom (Agaricus bisporus) crops (Crops 1, 2, 3) were grown to evaluate the effects of re-supplementing “spent” mushroom compost (MC) with the crystalline amino acids isoleucine (ile), leucine (leu), valine (val) and phenylalanine (phe) singly or in combination with Fermenten^® or SoyPlus^® on mushroom yield. Fermenten^® is a rumen fermentation enhancer while SoyPlus^® is a commercial delayed release mushroom nutrient. The most important single amino acid found for stimulating mushroom yield from 2nd break MC was ile. Crystalline ile added to 2nd break MC at 3.6% (dry wt) increased mushroom yields by 28.3% and 68.7% (average 48.5%) in Crops 1 and 2, respectively, compared to the non-supplemented control. In Crop 3, the addition of 5% or 10% ile to Fermenten^® and SoyPlus^® (3.6% total combined dry wt) did not significantly improve mushroom yield over treatments containing Fermenten^® or SoyPlus^® (3.6% total dry wt) alone. However, mixtures of equal quantities of Fermenten^®, ile and val significantly increased yield over Fermenten^® alone. Use of ile and val as supplements to stimulate mushroom yield from 2nd break MC is not economically viable because these amino acids are not commercially available at feed grade prices.     

A highly efficient and selective turn‐on fluorescent sensor for Hg2+, Ag+ and Ag nanoparticles based on a coumarin dithioate derivative

Based on chelation‐enhanced fluorescence, a new fluorescent coumarin derivative probe 3(1‐(7‐hydroxy‐4‐methylcoumarin)ethylidene)hydrazinecarbodithioate for Hg²⁺, Ag⁺ and Ag nanoparticles is reported. Fluorescent probe acts as a rapid and highly selective “off–on” fluorescent probe and fluorescence enhancement by factors 5 to12 times was observed upon selective complexation with Hg²⁺, Ag⁺ and Ag nanoparticles. The molar ratio plots indicated the formation of 1:1 complexes between Hg²⁺ and Ag⁺ with the probe. The linear response range covers a concentration range 0.1 × 10^–5–1.9 × 10^–5 mol/L, 0.1 × 10^–5–2.3 × 10^–5 mol/L and 0.146 × 10^–12–2.63 × 10^–12 mol/L for Hg²⁺, Ag⁺ and Ag nanoparticles, respectively. The interference effect of some anions and cations was also tested. Copyright © 2013 John Wiley & Sons, Ltd.     

Synthesis of mitochondrial DNA in spermatocytes of Rhynchosciara hollaenderi

During the mid to late 4th instar period of larval development, the mitochondria of Rhynchosciara spermatocytes undergo highly characteristic morphological changes. In late meiosis the enlarged mitochondria fuse to form a single mitochondrial element which will ultimately extend the length of the spermatid tail. Our studies have shown that synthesis of a circular DNA occurs during this period of mitochondrial “differentiation.” This DNA has a density of 1.681 g/cm³; and its synthesis cannot be detected in somatic tissues such as salivary gland, fat body, or gastric cecum. From analysis of DNA extracted from mitochondrial pellets, we have shown that the circular DNA is associated with the mitochondria. The contour length of the mitochondrial DNA is 9 μm, equivalent to a molecular weight of 18 × 10⁶. Although most metazoan mitochondrial DNAs exhibit contour lengths of approximately 5 μm (10 × 10⁵ daltons), there is no extractable 5 μm circular DNA in these spermatocytes. Therefore, we conclude that either Rhynchosciara spermatocytes possess a distinct 9 μm mitochondrial DNA or that the spermatocyte mitochondrial DNA represents dimers of 5 μm monomers.