Topochemistry of physical and chemical pretreatments of biomass as investigated by FE-SEM, XPS and ToF-SIMS

Surface chemistry is of great importance in plant biomass engineering and applications. The surface chemical composition of biomass which includes lignin, carbohydrates and extractives influences its interactions with chemical agents, such as pulp processing/papermaking chemicals, or enzymes for different purposes. In this thesis, the changes in the surface chemical composition of lignocellulosic biomass after physical modification for the improvement of resulting paper properties and chemical treatment for the enhancement of enzymatic hydrolysis were investigated. Low consistency (LC) refining was used as physical treatment of bleached softwood and hardwood pulp samples, and the surface chemistry of refined samples was investigated. The refined pulp was analysed as whole pulp while the fines-free fibre samples were characterized separately. The fines produced in LCrefining contributed to an enlarged surface specific area as well as the change of surface coverage by lignin and extractives, as investigated by X-ray photoelectron spectroscopy (XPS). The surface coverage by lignin of the whole pulp decreased after refining while the surface coverage by extractives increased both for pine and eucalyptus. In the case of pine, the removal of fines resulted in reduction of the surface coverage by extractives, while the surface coverage by lignin increased on fibre sample (without fines). In the case of eucalyptus, the surface coverage by lignin of fibre samples decreased after the removal of fines. In addition, the surface distribution of carbohydrates, lignin and extractives of pine and eucalyptus samples was determined by Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS). LC-refining increased the amounts of pentose, hexose and extractives on the surface of pine samples. ToF-SIMS also gave clear evidence about xylan deposition and reduction of surface lignin distribution on the fibre of eucalyptus. However, the changes in the surface chemical composition during the physical treatment has led to an increase in the adsorption of fluorescent whitening agents (FWAs) on fibres due to a combination of electro-static forces, specific surface area of fibres and hydrophobic interactions. Various physicochemical pretreatments were conducted on wood and non-wood biomass for enhancing enzymatic hydrolysis of polysaccharides, and the surface chemistry of the pretreated and enzymatically hydrolysed samples was investigated by field emission scanning electron microscopy (FE-SEM), XPS and ToF-SIMS. A hydrotrope was used as a relatively novel pretreatment technology both in the case of wood and non-wood biomass. For comparison, ionic liquid and hydrothermal pretreatments were applied on softwood and hardwood as well. Thus, XPS analysis showed that the surface lignin was more efficiently removed by hydrotropic pretreatment compared to ionic liquid or hydrothermal pretreatments. SEM analysis also found that already at room temperature the ionic liquid pretreatments were more effective in swelling the fibres compared with hydrotropic pretreatment at elevated temperatures. The enzymatic hydrolysis yield of hardwood was enhanced due to the decrease in surface coverage of lignin, which was induced by hydrotropic treatment. However, hydrotropic pretreatment was not appropriate for softwood because of the predominance of guaiacyl lignin structure in this material. In addition, the reduction of surface lignin and xylan during pretreatment and subsequent increase in cellulose hydrolysis by enzyme could be observed from ToF-SIMS results. The characterisation of the non-wood biomass (e.g. sugarcane bagasse and common reed) treated by hydrotropic method, alkaline and alkaline hydrogen peroxide pretreatments were carried out by XPS and ToF-SIMS. According to the results, the action for the removal of the surface lignin of non-wood biomass by hydrotropic pretreatment was more significant compared to alkaline and alkaline hydrogen peroxide pretreatments, although a higher total amount of lignin could be removed by alkaline and alkaline hydrogen peroxide pretreatment. Furthermore, xylan could be remarkably more efficiently removed by hydrotropic method. Therefore, the glucan yield achieved from hydrotropic treated sample was higher than that from samples treated with alkaline or alkaline hydrogen peroxide. Through the use of ToF-SIMS, the distribution and localization of lignin and carbohydrates on the surface of ignocelluloses during pretreatment and enzymatic hydrolysis could be detected, and xylan degradation during enzymatic hydrolysis could also be assessed. Thus, based on the results from XPS and ToF-SIMS, the mechanism of the hydrotropic pretreatment in improving the accessibility of enzymes to fibre and further ameliorating of the enzymatic saccharification could be better elucidated.

Influence of spray mixture volume and flight height on herbicide deposition in aerial applications on pastures

The objective of the present study was to analyze the influence of spray mixture volume and flight height on herbicide deposition in aerial applications on pastures. The experimental plots were arranged in a pasture area in the district of Porto Esperidião (Mato Grosso, Brazil). In all of the treatments, the applications contained the herbicides aminopyralid and fluroxypyr (Dominum) at the dose of 2.5 L c.p. ha-1, including the adjuvant mineral oil (Joint Oil) at the dose of 1.0 L and a tracer to determine the deposition by high-performance liquid chromatography (HPLC) (rhodamine at a concentration of 0.6%). The experiment consisted of nine treatments that comprised the combinations of three spray volumes (20, 30 and 50 L ha-1) and three flight heights (10, 30 and 40 m). The results showed that, on average, there was a tendency for larger deposits for the smallest flight heights, with a significant difference between the heights of 10 and 40 m. There was no significant difference among the deposits obtained with the different spray mixture volumes.

Reducing contact resistance in graphene devices

In this thesis, the contact resistance of graphene devices was investigated because high contact resistance is detrimental to the performance of graphene field-effect transistors (GFET). Method for increasing so-called edge-contact area was applied in device fabrication process, as few nanometers thick Ni layer was used as a catalytic etchant during the annealing process. Finally, Ni was also used as a metal for contact. GFETs were fabricated using electron beam lithography using graphene fabricated by chemical vapor deposition (CVD). Critical part of the fabrication process was to preserve the high quality of the graphene channel while etching the graphene at contact areas with Ni during the annealing. This was achieved by optimizing the combination of temperature and gas flows. The structural properties of graphene were studied using scanning electron microscopy, scanning confocal μ-Raman spectroscopy and optical microscopy. Evaluation of electric transport properties including contact resistance was carried out by transmission line method and four-probe method. The lowest contact resistance found was about at 350 Ωμm. In addition, different methods to transfer CVD graphene synthesized on copper were studied. Typical method using PMMA as a supporting layer leaves some residues after its removal, thus effecting on the performance of a graphene devices. In a metal assisted transfer method, metal is used as an interfacial layer between PMMA and graphene. This allows more effective removal of PMMA. However, Raman spectra of graphene transferred by metal assisted method showed somewhat lower quality than the PMMA assisted method

Application of cerium oxide thin films grown by atomic layer deposition for soot removal

The objective of the thesis is to study cerium oxide thin films grown by the atomic layer deposition (ALD) for soot removal. Cerium oxide is one of the most important heterogeneous catalysts and can be used in particulate filters and sensors in a diesel exhaust pipe. Its redox/oxidation properties are a key factor in soot oxidation. Thus, the cerium oxide coating can help to keep particulate filters and sensors clean permanently. The literature part of the thesis focuses on the soot removal, introducing the origin and structure of soot, reviewing emissions standards for diesel particulate matter, and presenting methods and catalysts for soot removal. In the experimental part the optimal ALD conditions for cerium oxide were found, the structural properties of cerium oxide thin films were analyzed, and the catalytic activity of the cerium oxide for soot oxidation was investigated. Studying ALD growth conditions of cerium oxide films and determining their critical thickness range are important to maximize the catalytic performance operating at comparatively low temperature. It was found that the cerium oxide film deposited at 300 °C with 2000 ALD cycles had the highest catalytic activity. Although the activity was still moderate and did not decrease the soot oxidation temperature enough for a real-life application. The cerium oxide thin film deposited at 300 °C has a different crystal structure, surface morphology and elemental composition with a higher Ce3+ concentration compared to the films deposited at lower temperatures. The different properties of the cerium oxide thin film deposited at 300 °C increase the catalytic activity most likely due to higher surface area and addition of the oxygen vacancies.

Artificial Ribonucleases: Oligonucleotides Conjugated with Metal Ion Chelates of Azacrowns

Ribonucleic acid (RNA) has many biological roles in cells: it takes part in coding, decoding, regulating and expressing of the genes as well as has the capacity to work as a catalyst in numerous biological reactions. These qualities make RNA an interesting object of various studies. Development of useful tools with which to investigate RNA is a prerequisite for more advanced research in the field. One of such tools may be the artificial ribonucleases, which are oligonucleotide conjugates that sequence-selectively cleave complementary RNA targets. This thesis is aimed at developing new efficient metal-ion-based artificial ribonucleases. On one hand, to solve the challenges related to solid-supported synthesis of metal-ion-binding conjugates of oligonucleotides, and on the other hand, to quantify their ability to cleave various oligoribonucleotide targets in a pre-designed sequence selective manner. In this study several artificial ribonucleases based on cleaving capability of metal ion chelated azacrown moiety were designed and synthesized successfully. The most efficient ribonucleases were the ones with two azacrowns close to the 3´- end of the oligonucleotide strand. Different transition metal ions were introduced into the azacrown moiety and among them, the Zn2+ ion was found to be better than Cu2+ and Ni2+ ions.

Een eenfalligh Kennedoom af nödtorftelighe articklar vthdraghne aff then Helga schrifft / Laurentius Olai Gestricius. (Coll. 762, Aholansaari Foundation's deposition)

Quire structure: 9xIV⁷² + (IV–1)⁷⁹. Text in one column, on (mostly) 26–33 lines, not ruled. Catchwords frequently used at the foot of each page to indicate the next word when a sentence continues on the next page. Not foliated. Gothic Cursive in one saec. XVI² hand. The first initial of the book has been touched with what looks like red pencil. This may be a later addition, as also the green tint to the outer edges of the block. Titles and rubrics distinguished, if at all, through layout only. A note fol. [47]v (see also the main text on fol. [31]v) indicates that the text was copied in 1580. The Anti-Papist poem mentions the Jesuit Antonio Possevino, active in Sweden in 1577–1580 (Kiiskinen ed. 2010, 25, 27). The texts appear to be copies of printed works, with the possible exception of the Anti-Papist poem. The publication of Eric Falck’s Een Tröstbook is known, but apparently no printed copies survive; Laurentius Olai Gestricius’ catechism is otherwise unknown. He was a teacher in Gävle from 1557 or 1558, then curate of Västerås from 1561 and of Stockholm in 1562, where he died in 1565 (Kiiskinen ed. 2010, 15, 349; Collijn ed. 1927–1938, vol. 2, 324).

An acid-sensing ion channel that detects ischemic pain

Ischemic pain occurs when there is insufficient blood flow for the metabolic needs of an organ. The pain of a heart attack is the prototypical example. Multiple compounds released from ischemic muscle likely contribute to this pain by acting on sensory neurons that innervate muscle. One such compound is lactic acid. Here, we show that ASIC3 (acid-sensing ion channel #3) has the appropriate expression pattern and physical properties to be the detector of this lactic acid. In rats, it is expressed only in sensory neurons and then only on a minority (~40%) of these. Nevertheless, it is expressed at extremely high levels on virtually all dorsal root ganglion sensory neurons that innervate the heart. It is extraordinarily sensitive to protons (Hill slope 4, half-activating pH 6.7), allowing it to readily respond to the small changes in extracellular pH (from 7.4 to 7.0) that occur during muscle ischemia. Moreover, both extracellular lactate and extracellular ATP increase the sensitivity of ASIC3 to protons. This final property makes ASIC3 a "coincidence detector" of three molecules that appear during ischemia, thereby allowing it to better detect acidosis caused by ischemia than other forms of systemic acidosis such as hypercapnia.

Solid-state reference and ion-selective electrodes : towards portable potentiometric sensing

Potentiometric sensors are very attractive tools for chemical analysis because of their simplicity, low power consumption and low cost. They are extensively used in clinical diagnostics and in environmental monitoring. Modern applications of both fields require improvements in the conventional construction and in the performance of the potentiometric sensors, as the trends are towards portable, on-site diagnostics and autonomous sensing in remote locations. The aim of this PhD work was to improve some of the sensor properties that currently hamper the implementation of the potentiometric sensors in modern applications. The first part of the work was concentrated on the development of a solid-state reference electrode (RE) compatible with already existing solid-contact ion-selective electrodes (ISE), both of which are needed for all-solid-state potentiometric sensing systems. A poly(vinyl chloride) membrane doped with a moderately lipophilic salt, tetrabutylammonium-tetrabutylborate (TBA-TBB), was found to show a satisfactory stability of potential in sample solutions with different concentrations. Its response time was nevertheless slow, as it required several minutes to reach the equilibrium. The TBA-TBB membrane RE worked well together with solid-state ISEs in several different situations and on different substrates enabling a miniature design. Solid contacts (SC) that mediate the ion-to-electron transduction are crucial components of well-functioning potentiometric sensors. This transduction process converting the ionic conduction of an ion-selective membrane to the electronic conduction in the circuit was studied with the help of electrochemical impedance spectroscopy (EIS). The solid contacts studied were (i) the conducting polymer (CP) poly(3,4-ethylienedioxythiophene) (PEDOT) and (ii) a carbon cloth having a high surface area. The PEDOT films were doped with a large immobile anion poly(styrene sulfonate) (PSS-) or with a small mobile anion Cl-. As could be expected, the studied PEDOT solid-contact mediated the ion-toelectron transduction more efficiently than the bare glassy carbon substrate, onto which they were electropolymerized, while the impedance of the PEDOT films depended on the mobility of the doping ion and on the ions in the electrolyte. The carbon cloth was found to be an even more effective ion-to-electron transducer than the PEDOT films and it also proved to work as a combined electrical conductor and solid contact when covered with an ion-selective membrane or with a TBA-TBB-based reference membrane. The last part of the work was focused on improving the reproducibility and the potential stability of the SC-ISEs, a problem that culminates to the stability of the standard potential E°. It was proven that the E° of a SC-ISE with a conducting polymer as a solid contact could be adjusted by reducing or oxidizing the CP solid contact by applying current pulses or a potential to it, as the redox state of the CP solid-contact influences the overall potential of the ISE. The slope and thus the analytical performance of the SC-ISEs were retained despite the adjustment of the E°. The shortcircuiting of the SC-ISE with a conventional large-capacitance RE was found to be a feasible instrument-free method to control the E°. With this method, the driving force for the oxidation/reduction of the CP was the potential difference between the RE and the SC-ISE, and the position of the adjusted potential could be controlled by choosing a suitable concentration for the short-circuiting electrolyte. The piece-to-piece reproducibility of the adjusted potential was promising, and the day-today reproducibility for a specific sensor was excellent. The instrumentfree approach to control the E° is very attractive considering practical applications.

Green welding in practice

Efficient production and consumption of energy has become the top priority of national and international policies around the world. Manufacturing industries have to address the requirements of the government in relation to energy saving and ecologically sustainable products. These industries are also concerned with energy and material usage due to their rising costs. Therefore industries have to find solutions that can support environmental preservation yet maintain competitiveness in the market. Welding, a major manufacturing process, consumes a great deal of material and energy. It is a crucial process in improving a product’s life-cycle cost, strength, quality and reliability. Factors which lead to weld related inefficiencies have to be effectively managed, if industries are to meet their quality requirements and fulfil a high-volume production demand. Therefore it is important to consider some practical strategies in welding process for optimization of energy and material consumption. The main objective of this thesis is to explore the methods of minimizing the ecological footprint of the welding process and methods to effectively manage its material and energy usage in the welding process. The author has performed a critical review of the factors including improved weld power source efficiency, efficient weld techniques, newly developed weld materials, intelligent welding systems, weld safety measures and personnel training. The study lends strong support to the fact that the use of eco-friendly welding units and the quality weld joints obtained with minimum possible consumption of energy and materials should be the main directions of improvement in welding systems. The study concludes that, gradually implementing the practical strategies mentioned in this thesis would help the manufacturing industries to achieve on the following - reduced power consumption, enhanced power control and manipulation, increased deposition rate, reduced cycle time, reduced joint preparation time, reduced heat affected zones, reduced repair rates, improved joint properties, reduced post-weld operations, improved automation, improved sensing and control, avoiding hazardous conditions and reduced exposure of welder to potential hazards. These improvement can help in promotion of welding as a green manufacturing process.

Roll-to-roll atomic layer deposition process for flexible electronics applications

Atomic Layer Deposition (ALD) is the technology of choice where very thin and highquality films are required. Its advantage is its ability to deposit dense and pinhole-free coatings in a controllable manner. It has already shown promising results in a range of applications, e.g. diffusion barrier coatings for OLED displays, surface passivation layers for solar panels. Spatial Atomic Layer Deposition (SALD) is a concept that allows a dramatic increase in ALD throughput. During the SALD process, the substrate moves between spatially separated zones filled with the respective precursor gases and reagents in such a manner that the exposure sequence replicates the conventional ALD cycle. The present work describes the development of a high-throughput ALD process. Preliminary process studies were made using an SALD reactor designed especially for this purpose. The basic properties of the ALD process were demonstrated using the wellstudied Al2O3 trimethyl aluminium (TMA)+H2O process. It was shown that the SALD reactor is able to deposit uniform films in true ALD mode. The ALD nature of the process was proven by demonstrating self-limiting behaviour and linear film growth. The process behaviour and properties of synthesized films were in good agreement with previous ALD studies. Issues related to anomalous deposition at low temperatures were addressed as well. The quality of the coatings was demonstrated by applying 20 nm of the Al2O3 on to polymer substrate and measuring its moisture barrier properties. The results of tests confirmed the superior properties of the coatings and their suitability for flexible electronics encapsulation. Successful results led to the development of a pilot scale roll-to-roll coating system. It was demonstrated that the system is able to deposit superior quality films with a water transmission rate of 5x10-6 g/m2day at a web speed of 0.25 m/min. That is equivalent to a production rate of 180 m2/day and can be potentially increased by using wider webs. State-of-art film quality, high production rates and repeatable results make SALD the technology of choice for manufacturing ultra-high barrier coatings for flexible electronics.

Proteoliposomes as matrix vesicles' biomimetics to study the initiation of skeletal mineralization

During the process of endochondral bone formation, chondrocytes and osteoblasts mineralize their extracellular matrix by promoting the formation of hydroxyapatite (HA) seed crystals in the sheltered interior of membrane-limited matrix vesicles (MVs). Ion transporters control the availability of phosphate and calcium needed for HA deposition. The lipidic microenvironment in which MV-associated enzymes and transporters function plays a crucial physiological role and must be taken into account when attempting to elucidate their interplay during the initiation of biomineralization. In this short mini-review, we discuss the potential use of proteoliposome systems as chondrocyte- and osteoblast-derived MVs biomimetics, as a means of reconstituting a phospholipid microenvironment in a manner that recapitulates the native functional MV microenvironment. Such a system can be used to elucidate the interplay of MV enzymes during catalysis of biomineralization substrates and in modulating in vitro calcification. As such, the enzymatic defects associated with disease-causing mutations in MV enzymes could be studied in an artificial vesicular environment that better mimics their in vivo biological milieu. These artificial systems could also be used for the screening of small molecule compounds able to modulate the activity of MV enzymes for potential therapeutic uses. Such a nanovesicular system could also prove useful for the repair/treatment of craniofacial and other skeletal defects and to facilitate the mineralization of titanium-based tooth implants.

Thick Section Laser Beam Welding of Structural Steels: Methods for Improving Welding Efficiency

Laser beam welding (LBW) is applicable for a wide range of industrial sectors and has a history of fifty years. However, it is considered an unusual method with applications typically limited to welding of thin sheet metal. With a new generation of high power lasers there has been a renewed interest in thick section LBW (also known as keyhole laser welding). There was a growing body of publications during 2001-2011 that indicates an increasing interest in laser welding for many industrial applications, and in last ten years, an increasing number of studies have examined the ways to increase the efficiency of the process. Expanding the thickness range and efficiency of LBW makes the process a possibility for industrial applications dealing with thick metal welding: shipbuilding, offshore structures, pipelines, power plants and other industries. The advantages provided by LBW, such as high process speed, high productivity, and low heat input, may revolutionize these industries and significantly reduce the process costs. The research to date has focused on either increasing the efficiency via optimizing process parameters, or on the process fundamentals, rather than on process and workpiece modifications. The argument of this thesis is that the efficiency of the laser beam process can be increased in a straightforward way in the workshop conditions. Throughout this dissertation, the term “efficiency” is used to refer to welding process efficiency, specifically, an increase in efficiency refers an increase in weld’s penetration depth without increasing laser power level or decreasing welding speed. These methods are: modifications of the workpiece – edge surface roughness and air gap between the joining plates; modification of the ambient conditions – local reduction of the pressure in the welding zone; modification of the welding process – preheating of the welding zone. Approaches to improve the efficiency are analyzed and compared both separately and combined. These experimentally proven methods confirm previous findings and contribute additional evidence which expand the opportunities for laser beam welding applications. The focus of this research was primarily on the effects of edge surface roughness preparation and pre-set air gap between the plates on weld quality and penetration depth. To date, there has been no reliable evidence that such modifications of the workpiece give a positive effect on the welding efficiency. Other methods were tested in combination with the two methods mentioned above. The most promising - combining with reduced pressure method - resulted in at least 100% increase in efficiency. The results of this thesis support the idea that joining those methods in one modified process will provide the modern engineering with a sufficient tool for many novel applications with potential benefits to a range of industries.

Paper- and membrane-based ion-modulated electronics

Avhandlingen handlar om pappers- och membranbaserad jonmodulerad elektronik. Målet med forskningen har varit att utveckla billig, miljövänlig och brännbar elektronik, som kan användas i vardagliga engångsprodukter. Baskomponenterna som utvecklas och presenteras i avhandlingen är transistorer och kondensatorer. Mer komplicerad logisk kretselektronik demonstreras också med hjälp av dessa komponenter. Substraten som utnyttjas vid framställningen av dessa elektroniska komponenter är papper och membran. Dessa substrat är flexibla, hållbara, billiga, miljövänliga, etc. och därför väl anpassade för befintliga tryckteknologier. Själva baskomponenterna framställs sedan på dessa substrat genom att trycka flera skikt på varandra, där varje enskilt skikt är ett individuellt material. Detta är möjligt eftersom de organiska materialen som används i dessa komponenter är upplösta i ett lösningsmedel och kan därmed tryckas på samma sätt som ett vanligt bläck. Ett tredimensionellt objekt kan på detta sätt framställas. I avhandlingen presenteras flera olika typer av transistorer, men den gemensamma nämnaren bland dessa är att isolatorn är en jonledare. Denna, ganska ovanliga, transistormodellen har den stora fördelen att lågspänningskomponenter kan relativt enkelt framställas. Det som är speciellt med våra transistorer är att vi har använt miljövänliga jonledare. Detta, bl.a., leder till att våra komponenter visar både god prestanda, tillika som de är miljövänliga. I avhandlingen demonstrerar vi även tryckta superkondensatorer, en motsvarighet till laddningsbara batterier, konstruerade på papper med aktiverat kol och miljövänliga jonledare. De mest komplicerade logiska kretsar som demonstreras i denna avhandling är ring-oscillatorer och 1-bits-minnen konstruerade på papper. --------------------------------------------- Väitöskirja käsittelee paperille ja polymeerikalvolle tulostettua ionimoduloitua elektroniikkaa. Tutkimuksen tavoitteena oli kehittää edullista, ympäristöystävällistä ja polttokelpoista elektroniikkaa, jota voidaan käyttää esim. tavanomaisissa kertakäyttötuotteissa. Väitöskirjassa esitellään erilaisia transistoreita ja kondensaattoreita. Näitä elektronisia peruskomponentteja käyttäen demonstroidaan myös monimutkaisempia loogisia piirejä. Komponenttien valmistuksessa alustana käytettiin paperia ja polymeerikalvoa. Valitut alustat ovat joustavia ja kestäviä, ja ovat siksi hyvin yhteensopivia olemassa olevien tulostusmenetelmien kanssa. Peruskomponentit valmistettiin tulostamalla eri materiaaleja päällekkäin. Komponenteissa käytettävät orgaaniset aineet ovat liuenneessa muodossa musteessa, joka voidaan tulostaa samalla periaatteella kuin mikä tahansa normaali muste. Tällä menetelmällä voidaan valmistaa myös kolmiulotteisia tuotteita. Väitöskirjassa esitellään useita erityyppisiä transistoreita, joissa yhdistävänä tekijänä on ionisesti johtava eriste. Tällaista suhteellisen harvinaista transistorityyppiä käyttämällä voidaan mahdollistaa matala-jännitteisten komponenttien yksinkertainen valmistus. Valmistettujen transistoreiden etu on ionisten nesteiden ympäristöystävällisyys. Elektroniset komponentit ovat täten hyviä suorituskyvyltään, mutteivät haitallisia ympäristölle. Väitöskirjassa demonstroidaan myös tulostettujen superkondensaattoreiden, eli ladattavien paristojen vastineiden, valmistus paperille aktiivihiiltä ja ionisia nesteitä käyttäen. Kaikkein monimutkaisimmat loogiset piirit, jotka tässä väitöskirjassa esitellään, ovat rengasoskillaattorit sekä 1-bittinen paperille valmistettu muisti.

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.