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.

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.

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.

Electroactive ion exchange membranes based on conducting polymers

Ion exchange membranes are indispensable for the separation of ionic species. They can discriminate between anions and cations depending on the type of fixed ionic group present in the membrane. These conventional ion exchange membranes (CIX) have exceptional ionic conductivity, which is advantageous in various electromembrane separation processes such as electrodialysis, electrodeionisation and electrochemical ion exchange. The main disadvantage of CIX membranes is their high electrical resistance owing to the fact that the membranes are electronically non conductive. An alternative can be electroactive ion exchange membranes, which are ionically and electronically conducting. Polypyrrole (PPy) is a type of electroactive ion exchange material as well as a commonly known conducting polymer. When PPy membranes are repeatedly reduced and oxidised, ions are pumped through the membrane. The main aim of this thesis was to develop electroactive cation transport membranes based on PPy for the selective transport of divalent cations. Membranes developed composed of PPy films deposited on commercially available support materials. To carry out this study, cation exchange membranes based on PPy doped with immobile anions were prepared. Two types of dopant anions known to interact with divalent metal ions were considered, namely 4-sulphonic calix[6]arene (C6S) and carboxylated multiwalled carbon nanotubes (CNT). The transport of ions across membranes containing PPy doped with polystyrene sulphonate (PSS) and PPy doped with para-toluene sulphonate (pTS) was also studied in order to understand the nature of ion transport and permeability across PPy(CNT) and PPy(C6S) membranes. In the course of these studies, membrane characterisation was performed using electrochemical quartz crystal microbalance (EQCM) and scanning electron microscopy (SEM). Permeability of the membranes towards divalent cations was explored using a two compartment transport cell. EQCM results demonstrated that the ion exchange behaviour of polypyrrole is dependent on a number of factors including the type of dopant anion present, the type of ions present in the surrounding medium, the scan rate used during the experiment and the previous history of the polymer film. The morphology of PPy films was found to change when the dopant anion was varied and even when the thickness of the film was altered in some cases. In nearly all cases the permeability of the membranes towards metal ions followed the order K+ > Ca2+ > Mn2+. The one exception was PPy(C6S), for which the permeability followed the order Ca2+ ≥ K+ > Mn2+ > Co2+ > Cr3+. The above permeability sequences show a strong dependence on the size of the metal ions with metal ions having the smallest hydrated radii exhibiting the highest flux. Another factor that affected the permeability towards metal ions was the thickness of the PPy films. Films with the least thickness showed higher metal ion fluxes. Electrochemical control over ion transport across PPy(CNT) membrane was obtained when films composed of the latter were deposited on track-etched Nucleopore® membranes as support material. In contrast, the flux of ions across the same film was concentration gradient dependent when the polymer was deposited on polyvinylidene difluoride membranes as support material. However, electrochemical control over metal ion transport was achieved with a bilayer type of PPy film consisting of PPy(pTS)/PPy(CNT), irrespective of the type of support material. In the course of studying macroscopic charge balance during transport experiments performed using a two compartment transport cell, it was observed that PPy films were non-permselective. A clear correlation between the change in pH in the receiving solution and the ions transported across the membrane was observed. A decrease in solution pH was detected when the polymer membrane acted primarily as an anion exchanger, while an increase in pH occurred when it functioned as a cation exchanger. When there was an approximately equal flux of anions and cations across the polymer membrane, the pH in the receiving solution was in the range 6 - 8. These observations suggest that macroscopic charge balance during the transport of cations and anions across polypyrrole membranes was maintained by introduction of anions (OH-) and cations (H+) produced via electrolysis of water.

Pyridyyliryhmän sisältävien erotusmateriaalien ominaisuudet ja soveltaminen hydrometallurgiassa

Diplomityössä tutkittiin silikarunkoisen, pyridyyliryhmän sisältävän erotusmateriaalin kykyä erottaa selektiivisesti kuparia, nikkeliä, kobolttia ja kadmiumia sinkkisulfaattiliuoksista. Erotuskykyä verrattiin kolonnikokein toiseen kaupalliseen polystyreenidivinyylibentseenirunkoiseen (PS-DVB) erotusmate-riaaliin, jonka funktionaalinen ryhmä on samantyyppinen. Silikarunkoisen erotusmateriaalin happo-emäsominaisuuksia selvitettiin titrauksin. Metallien sitoutumisen kinetiikkaa ja eluointia verrattiin PS-DVB-runkoisen erotus-materiaalin kirjallisuudessa esitettyihin tuloksiin. Lisäksi määritettiin kummankin erotusmateriaalin partikkelikokojakaumat. Silikarunkoisen materiaalin havaittiin turpoavan noin 4 % muutettaessa se vapaastaemäsmuodosta happomuotoon. Turpoaminen oli huomattavasti vähäisempää kuin PS-DVB-runkoisella materiaalilla. Silikarunkoisen erotus-materiaalin titrauksen tuloksena voitiin todeta, että se oli heikosti emäksinen. Titrauskäyrä muistutti PS-DVB-runkoisen erotusmateriaalin titrauskäyrää, vaikka erotusmateriaalien protonoitumisalueet olivat hieman erilaiset. Tämä johtuu siitä, että silikarunkoisen materiaalin funktionaaliset ryhmät poikkeavat rakenteeltaan hieman PS-DVB-runkoisesta materiaalista. Tasapainokokeet osoittivat, että silikarunkoinen erotusmateriaali adsorboi tutkituista metalleista eniten kuparia ja nikkeliä ja vähiten sinkkiä. Kaikkien tutkittujen metallien eluointi silikarunkoisesta erotusmateriaalista onnistui rikkihapolla toisin kuin PS-DVB-runkoisesta erotusmateriaalista, jonka regenerointiin tarvitaan rikkihappoa tai ammoniumhydroksidia riippuen siitä, mitä metalleja siihen on ladattu.

Stabilization of the ionic form of weak acid cation exchange resins

Weak acid cation exchange (WAC) resins are used in the chromatographic separation of betaine from vinasse, a by-product of sugar industry. The ionic form of the resin determines the elution time of betaine. When a WAC-resin is in hydrogen form, the retention time of betaine is the longest and betaine elutes as the last component of vi-nasse from the chromatographic column. If the feed solution contains salts and its pH is not acidic enough to keep the resin undissociated, the ionic form of the hydrogen form resin starts to alter. Vinasse contains salts and its pH is around 5, it also contains weak acids. To keep the metal ion content (Na/H ratio) of the resin low enough to ensure successful separation of betaine, acid has to be added to either eluent (water) or vinasse. The aim of the present work was to examine by laboratory experiments which option requires less acid. Also the retention mechanism of betaine was investigated by measuring retention volumes of acetic acid and choline in different Na/H ratios of the resin. It was found that the resulting ionic form of the resin is the same regardless of whether the regeneration acid is added to the eluent or the feed solution (vinasse). Be-sides the salt concentration and the pH of vinasse, also the concentration of weak acids in the feed affects the resulting ionic form of the resin. The more buffering capacity vinasse has, the more acid is required to keep the ionic form of the resin desired. Vinasse was found to be quite strong buffer solution, which means relatively high amounts of acid are required to prevent the Na/H ratio from increasing too much. It is known that the retention volume of betaine decreases significantly, when the Na/H ratio increases. This is assumed to occur, because the amount of hydrogen bonds between the carboxylic groups of betaine and the resin decreases. Same behavior was not found with acetic acid. Choline has the same molecular structure as betaine, but instead of carboxylic group it has hydroxide group. The retention volume of choline increased as the Na/H ratio of the resin increased, because of the ion exchange reaction between choline cation and dissociated carboxylic group of the resin. Since the retention behavior of choline on the resin is opposite to the behavior of be-taine, the strong affinity of betaine towards hydrogen form WAC-resin has to be based on its carboxylic group. It is probable that the quaternary ammonium groups also affect the behavior of the carboxylic groups of betaine, causing them to form hydrogen bonds with the carboxylic groups of the resin.

The Significance of Hydrogen Bonding Interactions in the Cleavage of RNA

RNA is essential for all living organisms. It has important roles in protein synthesis, controlling gene expression as well as catalyzing biological reactions. Chemically RNA is a very stable molecule, although in biological systems many agents catalyze the cleavage of RNA, such as naturally occurring enzymes and ribozymes. Much effort has been put in the last decades in developing highly active artificial ribonucleases since such molecules could have potential in the therapeutic field and provide tools for molecular biology. Several potential catalysts have emerged, but usually detailed cleavage mechanism remains unresolved. This thesis is aimed at clarifying mechanistic details of the cleavage and isomerization of RNA by using simpler nucleoside models of RNA. The topics in the experimental part cover three different studies, one concerning the mechanism of catalysis by large ribozymes, one dealing with the reactivity of modified and unmodified RNA oligonucleotides and one showing an efficient catalysis of the cleavage and isomerization of an RNA phosphodiester bond by a dinuclear metal ion complex. A review of the literature concerning stabilization of the phosphorane intermediate of the hydrolysis and isomerization of RNA phosphodiester bond is first presented. The results obtained in the experimental work followed by mechanistic interpretations are introduced in the second part of the thesis. Especially the significance of hydrogen bonding interactions is discussed.

Preparative ion exchange for salt solutions

Työssä tutkittiin moniarvoisten metalliformiaattien valmistusta ioninvaihto-menetelmällä. Kirjallisuustutkimus käsitteleetunnettuja alumiiniformiaatin ja rautaformiaatin valmistusmenetelmiä, kationinvaihtohartsien ominaisuuksia, ioninvaihtohartsien selektiivisyyttä ja alumiinin, raudan, magnesiumin ja sinkin vesikemiaa. Laboratoriokokeiden avulla tutkittiin sinkki-, magnesium-, rauta(II)- ja alumiiniformiaattien valmistusta ioninvaihdolla. Kokeet suoritettiin kolonnissa, joka oli pakattu makrohuokoisella tai geelimäisellä vahvalla kationin-vaihtohartsilla. Hartsi vaihdettiin natriummuodosta metallimuotoon metallikloridi- tai metallisulfaattiliuoksella.Metalli eluoitiin hartsista natriumformiaatilla. Formiaattien valmistus onnistui makrohuokoista vahvaa kationinvaihtohartsia käyttämällä. Rauta(II)formiaatin valmistus oli vaikeampaa kuin muiden formiaattien, koska rauta(II) hapettui osittain rauta(III):ksi valmistuksen aikana. Alumiiniformiaattia valmistettiin käyttäen sekä makrohuokoista että geelimäistä hartsia. Makrohuokoisen hartsin havaittiin soveltuvan geelimäistä hartsia paremmin alumiiniformiaatin valmistukseen. Kungeelimäistä hartsia käytettiin, noin 30 % alumiinista jäi kiinni hartsiin eikä siten eluoitunut. Ioninvaihdon selektiivisyyskertoimien saamiseksi suoritettiin tasapainokokeita. Selektiivisyyskertoimia käytettiin ioninvaihtokolonnin dynaamisessa simuloinnissa. Ioninvaihdon simuloiminen dynaamisella kolonnimallilla onnistui hyvin.

Lentotuhkan fraktiointi sähkösuodattimella ja Ion Blast -menetelmällä

Diplomityö on osa YTI-tutkimuskeskuksessa vuosina 2002 - 2004 toteutettavaa Jätekompostit rakeiksi tuhkaseostuksella -käyttöarvon parantaminen -projektia. Työssä tutkittiin Etelä-Savon Energia Oy:n Pursialan voimalaitoksen lentotuhkan fraktioimista voimalaitoksen nykyisellä 3-kenttäisellä sähkösuodattimella ja pilot-mittakaavaisella Ion Blast -koelaitteistolla. Sähkösuodattimen koeajojen aikana muuteltiin sen ajotapaa mm. CBO -suhteen ja maksimijänniteasetuksen avulla. Ion Blast -koelaitteistolla tutkittiin mahdollisuuksia voimalaitoksen lentotuhkan puhdistamiseksi raskasmetalleista. Lentotuhkan hyötykäyttöä vaikeuttaa sen raskasmetallipitoisuuksien suuri vaihtelu. Ongelmallisin raskasmetalli puuperäisessä lentotuhkassa on kadmium, jonka lannoitelainsäädännön raja-arvo on tällä hetkellä 3 mg/kg. Sähkösuodattimella tehtyjen fraktiointikokeiden perusteella voidaan todeta raskasmetallipitoisuuksien olevan pienimmillään sähkösuodattimen 1-kentässä ja suurimmillaan 3-kentässä. Tämä johtuu siitä, että 1-kenttään kerääntyy hiukkaskooltaan suurimmat lentotuhkahiukkaset ja 3-kentässä on mukana enemmän pienhiukkasia sisältävää tuhkaa. Lannoitteeksi menevän tuhkan Cd-pitoisuutta voidaan vähentää parhaimmillaan jopa 70 % sähkösuodattimella fraktioimalla. Muiden raskasmetallien pitoisuudet eivät vähene aivan yhtä paljon. Sähkösuodattimella voidaan tulosten perusteella fraktioida lentotuhkaa. Sähkösuodattimella ei kuitenkaan voida varmasti saavuttaa alle 3 mg/kg Cd-pitoisuuksia polttoaineen laadunvaihtelun vuoksi. Ion Blast -koelaitteiston tulokset tukevat sähkösuodattimella tehtyjä kokeita. Erottimen jännitteen kasvaessa raskasmetalleja sisältävien hiukkasten erotusaste kasvaa. Ion Blast -laitteistolla tehdyissä kokeissa myös Cd-pitoisuus oli korkeimmillaan pienimmän raeluokan hiukkasissa ja laski sitten raeluokan suurentuessa. Ion Blast -laitteisto ei kuitenkaan sellaisenaan ole hyvä fraktiointiin. Se on liian tehokas, jolloin se puhdistaa tehokkaasti myös raskasmetalleja sisältävät pienhiukkaset. Jos laitetta aiotaan käyttää fraktiointiin, tulisi sen rakennetta muuttaa.

Emission, kinetic and magnetic phenomena in rare-earth and transition metal doped ZnSe single crystals

In this work emission, optical, electrical and magnetic properties of the d- and f- elements doped zinc selenide crystals were investigated within a wide temperature range. Doping was performed in various technological processes: during the growth by chemical vapor transport method; by thermal diffusion from the Bi or Zn melt. Concentration of the doping impurity in the crystals was controlled by amount of the dopant in the source material or by its concentration in the doping media. Special interest in the work was paid to the influence of the different concentrations of Cr and Yb impurities on ZnSe crystals’ properties, correlations between observed effects and similarities with the Ni, Mn and Gd dopants are analysed. Possibility of formation of the excitons bound to the doping d-ions was shown. In contrast to this, it was observed that f-elements do not bound excitons, but prevent formation of excitons bound to some uncontrolled impurities. A mechanism of Cr doping impurity interaction with background impurities and zinc selenide structural defects was proposed based on experimental data. An assumption about resonant energy transfer between double charged chromium ions and complexes based on crystals’ vacancy defects was made. A correlation between emission and magnetic properties of the d- ions doped samples was established. Based on this correlation a mechanism explaining the concentration quench of the emission was proposed. It was found that f-ions bind electrically active shallow and deep donor and acceptor states of background impurity to electrically neutral complexes. This may be observed as “purification” of ZnSe crystals by doping with the rare-earth elements, resulting i tendency of the properties of f-ion doped crystals to the properties of intrinsic crystals, but with smaller concentration of uncontrolled native and impurity defects. A possible interpretation of this effect was proposed. It was shown that selenium substituting impurities decrease efficiency of the Yb doping. Based on this experimental results an attempt to determine ytterbium ion surroundings in the crystal lattice was made. It was shown that co-doping of zinc selenide crystals with the d- and f- ions leads to the combination of the impurities influence on the material’s properties. On the basis of obtained data an interaction mechanism of the d- and f-elements co-dopants was proposed. Guided by the model of the ytterbium ion incorporation in the selenide sublattice of the ZnSe crystals, an assumption about stabilization of single charged chromium ions in the zinc sublattice crystal nodes, by means of formation of the local charge compensating clusters, was made.

Arsenic and heavy metal concentrations in agricultural soils in South Savo province

Selostus: Etelä-Savon viljelysmaan arseeni- ja raskasmetallipitoisuudet

Heavy-metal pollution and remediation of forest soil around the Harjavalta Cu-Ni smelter, in SW Finland

Abstract

Logistics Management in China's Development Zones - Finnish Metal Industry Perspective

Alikehittynyt infrastruktuuri, tiukat säädökset ja säädösten tulkitseminen, sekä monimutkaiset verotuskäytännöt ovat aiheuttaneet ongelmia suomalaisille Alikehittynyt infrastruktuuri, tiukat säädökset ja säädösten tulkitseminen, sekä monimutkaiset verotuskäytännöt ovat aiheuttaneet ongelmia suomalaisille yrityksille Kiinassa. Tutkimuksen perusteella yritykset eivät pysty vaikuttamaan infrastruktuurin kehittymiseen tai säädösten implementointiin, mutta ylläpitämällä suhteita ja valitsemalla oikeat partnerit yritykset pystyvät hallitsemaan ongelma-alueitaan. Etenkin ulkomaalaisille yrityksille oikean logistiikkaoperaattorin valinta on tärkeätä ja huomioon ottaen palvelutason, kulttuuritaustan sekä kansainväliset operaatiot on ulkomaalaisten yritysten tehokkaampaa käyttää kansainvälisiä operaattoreita kuin paikallisia toimijoita, jotkaovat usein halvempia, mutta eivät pysty toimimaan kansainvälisellä tasolla. Vientiin keskittyneiden yritysten tulisi sijoittua vapaakauppa-alueille tai vientiin painottuneille teollisuusalueille. Kyseisillä alueilla liiketoiminta mannermaahan on rajoitettu, eivätkä alueet täten sovellu yrityksille, jotka ovat keskittyneet Kiinan markkinoille. Paikallisesti operoivien yritysten tulisi sijoittua normaaleihin teollisuuspuistoihin ja käyttää tullin valvomia varastoja tukemaan kansainvälisiä toimintojaan.Tulisi myös muistaa etteivät kiinalaiset teollisuuspuistot täytä kansainvälisiä kriteerejä, joten säädöksiin on tärkeätä tutustua huolella jamielipiteitä kerätä toisilta yrityksiltä. Kiinassa merkittävimmät logistiikkaongelmat ilmenevät tuonnin ja viennin yhteydessä, jolloin säädökset ja toimintamallit ovat kontrolloidumpia. Etenkin tullaus- ja arvonlisävero ongelmat liittyvät kiinteästi tuonti- ja vientiprosessiin. Tutkimuksen tulokset osoittivat, että tullausprosessi tehostuu yhteistyön ja koulutuksen kautta, mutta arvonlisäverosta aiheutuvien kustannusten minimointi vaatii logistiikkapuistojen käyttöä. Mikäli asiakas haluaa tehdä tullauksen kotiprovinssissaan tai yritys tekee kauppaa ALV -vapautettujen yritysten kanssa, tulisi logistiikkapuistojen käyttöä lisätä. Käytettäessä logistiikkapuistoja yritykset välttävät tuotteiden kuljetukset Hongkongiin jatakaisin säästäen huomattavasti kustannuksissa ja toimitusajoissa. Logistiikkapuistoja on myös mahdollista käyttää ratkaisuna kasvaviin ja viivästyviin ALV palautuksiin. Tutkimuksen tulosten mukaan toimintaympäristö ja vientipainotteinen valmistus ohjaavat 3PL yritysten valintaa ja vaihtoehtoisten logistiikkapalvelujen implementointia. Etabloiduttaessavapaakauppa-alueille vientiin ja tuontiin liittyvät ongelmatekijät vahvistuvat sekä rajoitukset kiinan liiketoimintaan kasvavat, mikä tekee yhteistyönkansainvälisten logistiikkaoperaattoreiden kanssa välttämättömäksi ja kannustaa hyödyntämään logistiikkapuistoja.