Metal-Ion-Binding Oligonucleotides: High-Affinity Probes for Nucleic Acid Sequences

Small non-coding RNAs have numerous biological functions in cell and are divided into different classes such as: microRNA, snoRNA, snRNA and siRNA. MicroRNA (miRNA) is the most studied non-coding RNA to date and is found in plants, animals and some viruses. miRNA with short sequences is involved in suppressing translation of target genes by binding to their mRNA post-transcriptionally and silencing it. Their function besides silencing of the viral gene, can be oncogenic and therefore the cause of cancer. Hence, their roles are highlighted in human diseases, which increases the interest in using them as biomarkers and drug targets. One of the major problems to overcome is recognition of miRNA. Owing to a stable hairpin structure, chain invasion by conventional Watson-Crick base-pairing is difficult. One way to enhance the hybridization is exploitation of metal-ion mediated base-pairing, i. e. oligonucleotide probes that tightly bind a metal ions and are able to form a coordinative bonds between modified and natural nucleobases. This kind of metallo basepairs containing short modified oligonucleotides can also be useful for recognition of other RNA sequences containing hairpin-like structural motives, such as the TAR sequence of HIV. In addition, metal-ion-binding oligonucleotides will undoubtedly find applications in DNA-based nanotechnology. In this study, the 3,5-dimethylpyrazol-1-yl substituted purine derivatives were successfully incorporated within oligonucleotides, into either a terminal or non-terminal position. Among all of the modified oligonucleotides studied, a 2-(3,5-dimethylpyrazol-1-yl)-6-oxopurine base containing oligonucleotide was observed to bind most efficiently to their unmodified complementary sequences in the presence of both Cu2+ or Zn2+. The oligonucleotide incorporating 2,6-bis(3,5-dimethylpyrazol-1-yl)purine base also markedly increased the stability of duplexes in the presence of Cu2+ without losing the selectivity.

Voimalaitosten kattilaputkien sisäpuolisten kerrostumien paksuuden mittaaminen ultraäänimenetelmällä

Höyryvoimalaitoksen käyttöönotossa muodostuu kattilaputkien sisäpinnoille niitä korroosiolta suojaava ohut metallioksidikerros. Tämän kerroksen päälle kasvaa kattilan käytön aikana haitallista kerrostumaa paikallisen korroosion tai kattilavedessä olevien epäpuhtauksien kerääntymisen tai kiteytymisen seurauksena. Kerrostuma haittaa lämmönsiirtoa tulipesästä putkiseinämän läpi kattilaveteen. Putkien lämpötilan nousu suunniteltua korkeammaksi kasvattaa putkivaurioiden ja sisäpuolisen korroosion riskiä. Tästä johtuen paksuksi kasvaneet kerrostumat pyritään poistamaan happokäsittelyllä eli peittauksella ennen vaurioiden syntyä. Perinteisesti kerrostumapaksuus on määritetty kattilasta irrotetuista näyteputkista mikroskoopilla. Työn tavoitteena oli tutkia uudenlaisen ultraäänimittauksen teoriaa ja selvittää sen toimivuus höyrystinputkien kerrostumapaksuusmittauksissa. Lisäksi tavoitteena oli tutkia voimalaitoksen höyrystimen sisäpuolisten kerrostumien muodostumista ja niiden vaikutuksia sekä kattilan peittaustarpeen arviointia. Höyrystimen kerrostumien kasvunopeuteen vaikuttavat eniten voimalaitostyyppi, käytetty vesikemia ja kattilaveteen kulkeutuvien epäpuhtauksien määrä. Kasvunopeus vaihtelee laitosten välillä suuresti ja eroaa myös tulipesän eri kohdissa. Kattilaveden epäpuhtauspitoisuus ja kerrostumapaksuus vaikuttavat molemmat korroosiovaurioiden todennäköisyyteen. Peittauspaksuuden ohjearvoissa tulisi huomioida kattilan käyttöpaine, kattilatyyppi ja riski kattilaveden laadun heikkenemiselle. Putkinäytteistä ja laitoksilla suoritettujen mittauksien perusteella uusi ultraäänitekniikka tuottaa luotettavia tuloksia tavanomaisten kerrostumien mittauksessa. Vain yhdellä laitoksella esiintyi irtonaisen sakan kaltaista kerrostumaa, jota mittaus ei kyennyt havaitsemaan. Mittaustulokset kerrostumista tulipesän eri osissa antavat hyvän perustan peittaustarpeen arviointiin.

Recognition of nucleic acids by metal ion complexes

Metal-ion-mediated base-pairing of nucleic acids has attracted considerable attention during the past decade, since it offers means to expand the genetic code by artificial base-pairs, to create predesigned molecular architecture by metal-ion-mediated inter- or intra-strand cross-links, or to convert double stranded DNA to a nano-scale wire. Such applications largely depend on the presence of a modified nucleobase in both strands engaged in the duplex formation. Hybridization of metal-ion-binding oligonucleotide analogs with natural nucleic acid sequences has received much less attention in spite of obvious applications. While the natural oligonucleotides hybridize with high selectivity, their affinity for complementary sequences is inadequate for a number of applications. In the case of DNA, for example, more than 10 consecutive Watson-Crick base pairs are required for a stable duplex at room temperature, making targeting of sequences shorter than this challenging. For example, many types of cancer exhibit distinctive profiles of oncogenic miRNA, the diagnostics of which is, however, difficult owing to the presence of only short single stranded loop structures. Metallo-oligonucleotides, with their superior affinity towards their natural complements, would offer a way to overcome the low stability of short duplexes. In this study a number of metal-ion-binding surrogate nucleosides were prepared and their interaction with nucleoside 5´-monophosphates (NMPs) has been investigated by 1H NMR spectroscopy. To find metal ion complexes that could discriminate between natural nucleobases upon double helix formation, glycol nucleic acid (GNA) sequences carrying a PdII ion with vacant coordination sites at a predetermined position were synthesized and their affinity to complementary as well as mismatched counterparts quantified by UV-melting measurements.

Monitoring Directed Energy Deposition Processes in Additive Manufacturing

The purpose of this study is to find out how laser based Directed Energy Deposition processes can benefit from different types of monitoring. DED is a type of additive manufacturing process, where parts are manufactured in layers by using metallic powder or metallic wire. DED processes can be used to manufacture parts that are not possible to manufacture with conventional manufacturing processes, when adding new geometries to existing parts or when wanting to minimize the scrap material that would result from machining the part. The aim of this study is to find out why laser based DED-processes are monitored, how they are monitored and what devices are used for monitoring. This study has been done in the form of a literature review. During the manufacturing process, the DED-process is highly sensitive to different disturbances such as fluctuations in laser absorption, powder feed rate, temperature, humidity or the reflectivity of the melt pool. These fluctuations can cause fluctuations in the size of the melt pool or its temperature. The variations in the size of the melt pool have an effect on the thickness of individual layers, which have a direct impact on the final surface quality and dimensional accuracy of the parts. By collecting data from these fluctuations and adjusting the laser power in real-time, the size of the melt pool and its temperature can be kept within a specified range that leads to significant improvements in the manufacturing quality. The main areas of monitoring can be divided into the monitoring of the powder feed rate, the temperature of the melt pool, the height of the melt pool and the geometry of the melt pool. Monitoring the powder feed rate is important when depositing different material compositions. Monitoring the temperature of the melt pool can give information about the microstructure and mechanical properties of the part. Monitoring the height and the geometry of the melt pool is an important factor in achieving the desired dimensional accuracy of the part. By combining multiple different monitoring devices, the amount of fluctuations that can be controlled will be increased. In addition, by combining additive manufacturing with machining, the benefits of both processes could be utilized.

Metal oxides prepared through the nanocasting approach-mechanistic study, surface interactions and applications in separation

Mesoporous metal oxides are nowadays widely used in various technological applications, for instance in catalysis, biomolecular separations and drug delivery. A popular technique used to synthesize mesoporous metal oxides is the nanocasting process. Mesoporous metal oxide replicas are obtained from the impregnation of a porous template with a metal oxide precursor followed by thermal treatment and removal of the template by etching in NaOH or HF solutions. In a similar manner to the traditional casting wherein the product inherits the features of the mold, the metal oxide replicas are supposed to have an inverse structure of the starting porous template. This is however not the case, as broken or deformed particles and other structural defects have all been experienced during nanocasting experiments. Although the nanocasting technique is widely used, not all the processing steps are well understood. Questions over the fidelity of replication and morphology control are yet to be adequately answered. This work therefore attempts to answer some of these questions by elucidating the nanocasting process, pin pointing the crucial steps involved and how to harness this knowledge in making wholesome replicas which are a true replication of the starting templates. The rich surface chemistry of mesoporous metal oxides is an important reason why they are widely used in applications such as catalysis, biomolecular separation, etc. At times the surface is modified or functionalized with organic species for stability or for a particular application. In this work, nanocast metal oxides (TiO2, ZrO2 and SnO2) and SiO2 were modified with amino-containing molecules using four different approaches, namely (a) covalent bonding of 3-aminopropyltriethoxysilane (APTES), (b) adsorption of 2-aminoethyl dihydrogen phosphate (AEDP), (c) surface polymerization of aziridine and (d) adsorption of poly(ethylenimine) (PEI) through electrostatic interactions. Afterwards, the hydrolytic stability of each functionalization was investigated at pH 2 and 10 by zeta potential measurements. The modifications were successful except for the AEDP approach which was unable to produce efficient amino-modification on any of the metal oxides used. The APTES, aziridine and PEI amino-modifications were fairly stable at pH 10 for all the metal oxides tested while only AZ and PEI modified-SnO2 were stable at pH 2 after 40 h. Furthermore, the functionalized metal oxides (SiO2, Mn2O3, ZrO2 and SnO2) were packed into columns for capillary liquid chromatography (CLC) and capillary electrochromatography (CEC). Among the functionalized metal oxides, aziridinefunctionalized SiO2, (SiO2-AZ) showed good chemical stability, and was the most useful packing material in both CLC and CEC. Lastly, nanocast metal oxides were synthesized for phosphopeptide enrichment which is a technique used to enrich phosphorylated proteins in biological samples prior to mass spectrometry analysis. By using the nanocasting technique to prepare the metal oxides, the surface area was controlled within a range of 42-75 m2/g thereby enabling an objective comparison of the metal oxides. The binding characteristics of these metal oxides were compared by using samples with different levels of complexity such as synthetic peptides and cell lysates. The results show that nanocast TiO2, ZrO2, Fe2O3 and In2O3 have comparable binding characteristics. Furthermore, In2O3 which is a novel material in phosphopeptide enrichment applications performed comparably with standard TiO2 which is the benchmark for such phosphopeptide enrichment procedures. The performance of the metal oxides was explained by ranking the metal oxides according to their isoelectric points and acidity. Overall, the clarification of the nanocasting process provided in this work will aid the synthesis of metal oxides with true fidelity of replication. Also, the different applications of the metal oxides based on their surface interactions and binding characteristics show the versatility of metal oxide materials. Some of these results can form the basis from which further applications and protocols can be developed.

Droplet Deposition in the Last Stage of Steam Turbine

During the expansion of steam in turbine, the steam crosses the saturation line and hence subsequent turbine stages run under wet condition. The stages under wet condition run with low efficiency as compared to stages running with supersaturated steam and the life of the last stage cascade is reduced due to erosion. After the steam crosses the saturation line it does not condense immediately but instead it becomes supersaturated which is a meta-stable state and reversion of equilibrium results in the formation of large number of small droplets in the range of 0.05 - 1 μm. Although these droplets are small enough to follow the stream lines of vapor however some of the fog droplets are deposited on the blade surface. After deposition they coagulate into films and rivulets which are then drawn towards the trailing edge of the blade due to viscous drag of the steam. These large droplets in the range of radius 100 μm are accelerated by steam until they impact on the next blade row causing erosion. The two phenomenon responsible for deposition are inertial impaction and turbulent-diffusion. This work shall discuss the deposition mechanism in steam turbine in detail and numerically model and validate with practical data.