<p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-bidi-font-weight:bold'>M-DNA is a novel complex formed between DNA and transition metal ions under alkaline conditions.<span style='mso-spacerun:yes'>  </span>The unique properties of M-DNA were manipulated in order to rationally place metal ions at specific regions within a double-stranded DNA helix.<span style='mso-spacerun:yes'>   </span>Investigations using thermal denaturation profiles and the ethidium fluorescence assay illustrate that the pH at which M-DNA formation occurs is influenced heavily by the DNA sequence and base composition.<span style='mso-spacerun:yes'>  </span>For instance, DNA with a sequence consisting of poly[d(TG)d(CA)] is completely converted to M-DNA at pH 7.9 while DNA consisting entirely of poly[d(AT)] remains in the B-DNA conformation until a pH of 8.6 is reached.<span style='mso-spacerun:yes'>  </span>The pH at which M-DNA formation occurs is further decreased by the incorporation of 4-thiothymine (s⁴T).<span style='mso-spacerun:yes'>  </span>DNA oligomers with a mixed sequence composed of </span>half d(AT) and the other half d(TG)d(CA)<span style='mso-bidi-font-weight: bold'> showed that only 50% of the DNA is able to incorporate Zn²⁺ ions at pH 7.9.<span style='mso-spacerun:yes'>  </span>This suggests that only regions corresponding to the tracts of <span class=GramE>d(</span>TG)d(CA) are being transformed.<span style='mso-spacerun:yes'>   </span><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-fareast-language:ZH-CN'>Duplex DNA monolayers were self-assembled on gold through <span class=GramE>a</span> Au-S linkage and both B- and M-DNA conformations were studied using X-ray photoelectron spectroscopy (XPS) in order to better elucidate the location of the metal ions.<span style='mso-spacerun:yes'>  </span>The film thickness, density, elemental composition and ratios for samples were analyzed and compared.<span style='mso-spacerun:yes'>  </span>The DNA surface coverage, calculated from both XPS and electrochemical measurements, was <span class=GramE>approximately 1.2 x 10¹³molecules/cm²</span>for B-DNA.<span style='mso-spacerun:yes'>  </span>All samples showed distinct peaks for C 1s, O 1s, N 1s, P 2p and S 2p as expected for a thiol-linked DNA.<span style='mso-spacerun:yes'>  </span></span><span style='mso-bidi-font-weight: bold'>On addition of Zn²⁺ to form M-DNA the C 1s, P 2p and S 2p showed only small changes </span><span style='mso-fareast-language:ZH-CN'>while both the N 1s and O 1s spectra changed considerably.<span style='mso-spacerun:yes'>  </span>This result is consistent with Zn²⁺ interacting with oxygen on the phosphate backbone as well as replacing the imino protons of thymine (T) and guanine (G) in M-DNA.<span style='mso-spacerun:yes'>   </span>Analysis of the Zn 2p spectra also demonstrated that the concentration of Zn²⁺ present under M-DNA conditions is consistent with Zn²⁺ binding to both the phosphate backbone as well as replacing the imino protons of T or G in each base pair.<span style='mso-spacerun:yes'>  </span>After the M-DNA monolayer is washed with a buffer containing only Na⁺ the Zn²⁺ bound to the phosphate backbone is removed while the Zn²⁺ bound internally still remains. </span><span style='mso-bidi-font-weight:bold'>Variable angle x-ray photoelectron spectroscopy (VAXPS) was also used to examine monolayers consisting of mixed sequence oligomers.<span style='mso-spacerun:yes'>  </span>Preliminary results suggest that under M-DNA conditions, the zinc to phosphate ratio changes relative to the position of the <span class=GramE>d(</span>TG)d(CA) tract being at the top or bottom of the monolayer.<span style='mso-spacerun:yes'>  </span><span style='mso-spacerun:yes'> </span><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;text-indent:.5in;line-height:150%'><span style='mso-bidi-font-weight:bold'>Electrochemistry was also used to investigate the properties of M-DNA monolayers on gold and examine how the localization of metal ions affects the resistance through the DNA monolayer.<span style='mso-spacerun:yes'>  </span>T</span>he effectiveness of using the IrCl₆^2-/3-redox couple to investigate DNA monolayers and the potential advantages of this system over the standard Fe(CN)₆^3-/4- redox couple are demonstrated.<span style='mso-spacerun:yes'>  </span>B-DNA monolayers were converted to M-DNA by incubation in buffer containing 0.4 mM Zn²⁺ at pH 8.6 and studied by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and chronoamperometry (CA) with IrCl₆^2-/3-.<span style='mso-spacerun:yes'>  </span>^{<span style='mso-spacerun:yes'> </span>}Compared to B-DNA, M-DNA showed significant changes in CV, EIS and CA spectra.<span style='mso-spacerun:yes'>  </span>However, only small changes were observed when the monolayers were incubated in Mg²⁺at pH 8.6 or in Zn²⁺ at pH 6.0.<span style='mso-spacerun:yes'>  </span>The heterogeneous electron-transfer rate (<i style='mso-bidi-font-style:normal'>k</i>_ET) between the redox probe and the surface of a bare gold electrode was determined to be 5.7 x 10^-3 cm/s.<span style='mso-spacerun:yes'>  </span>For a B-DNA modified electrode, the <i style='mso-bidi-font-style:normal'>k</i>_ET through the monolayer was too slow to be measured.<span style='mso-spacerun:yes'>  </span>However, under M-DNA conditions, a <i style='mso-bidi-font-style:normal'>k</i>_ET of 1.5 x 10^-3 cm/s was reached.<span style='mso-spacerun:yes'>  </span>As well, the percent change in resistance to charge transfer (R_CT), measured by EIS, <span class=GramE>was</span> used to illustrate the dependence of M-DNA formation on pH.<span style='mso-spacerun:yes'>  </span>This result is consistent with Zn²⁺ ions replacing the imino protons on thymine and guanine residues.<span style='mso-spacerun:yes'>  </span>Also, at low pH values, the percent change in R_CT seems to be greater for <span class=GramE><span style='mso-bidi-font-weight:bold'>d(</span></span><span style='mso-bidi-font-weight: bold'>TG)₁₅d(CA)₁₅ compared to oligomers with mixed d(AT) and d(TG)d(CA) tracts.<span style='mso-spacerun:yes'>  </span></span>The IrCl₆^2-/3-redox couple was also effective in differentiating between single-stranded and double-stranded DNA during dehybridization and rehybridization experiments.<span style='mso-spacerun:yes'>  </span><span style='mso-bidi-font-weight:bold'><o:p></o:p></span></p>

Inspired by Poirier¡¦s mechanism of self-assembled monolayers (SAMs) formation, we realized that observation of the change of molecular orientation relative to the surface using a suitable spectroscopic method might be able to reveal the self ¡V assemblied processes. We mimicked the SAMs formation under UHV conditions, the Reflection Absorption Infrared Spectroscopy (RAIRS) and Temperature-Programmed Desorption / Reaction Spectrometry (TPD/R) were utilized to understand the adsorption, self-assembling and thermal stability after vapor desorption of 1H, 1H, 2H, 2H-perfluorodecanethiol on Cu(111). At 100K, the adsorption of 1H, 1H, 2H, 2H-perfluorodecanethiol was entirely molecular. As the surface was annealed above 220K, the cleavage of the S ¡V H bonds occurred to afford chemisorbed thiolates. By comparisons of spectra to the SAMs / Au(111) and the bulk compound, forming of an orderly and densely packed monolayer on Cu(111) was inferred. Focusing on room temperature deposition experiments, We found that the increase in ratios of I£h(CF2 ¡ü chain) (bands in 1300cm-1 ~ 1400 cm-1) to I£h(CF2 ¡æ chain) (bands in 1100cm-1 ~ 1300 cm-1) as a function of exposure implicates a transition from that the lying ¡V down geometry to the more upright orientation relative to the surface as we anticipated, the phase transformation concomitant with the SAMs formation could be identified by RAIRS. By TPD/R measurements, the molecular desorption occurred at 220K and 290K, corresponding to the condensed multilayer and a physisorbed layer on top of the chemisorbed monolayer, respectively. Furthermore, the monolayer would undergo the S ¡V C bond dissociation to sender surface ¡V bound semifluorinated alkyl groups and sulfur atoms. The semifluorinated decene and decane were evolved above 360K as results of £] ¡V hydride elimination and hydrogen addition.

Langmuir monolayers can be employed as simple model systems to study interactions at surfaces. Such investigations are important to fields ranging from biology to materials science. Herein, several aspects of these films and their associated water structure have been examined with vibrational sum frequency spectroscopy (VSFS). This second order nonlinear optical spectroscopy is particularly well suited for simultaneous investigations of the monolayer and the associated water structure with unprecedented surface specificity. The structures of these systems were altered through the control of experimental parameters including monolayer pressure, subphase temperature, pH and ionic content. Thermodynamic information about structural changes in a fatty amine monolayer's hydrophobic region was obtained by observation of the pressure and temperature dependence of the monolayer's solid to liquid phase transition. Further studies used the coordination of divalent cations to acid monolayers to perturb the water layers nearest to the film which enabled a better understanding of the water related VSFS features from these hydrophilic interfaces. Information from both the monolayer and water structure was then combined in order to examine the role of water in mediating ion-biomaterial interactions, often expressed in terms of the Hofmeister series.

Herein are presented collective studies of amino acid-based surfactants, also known as lipoamino acids, at liquid interfaces. Chapter III describes an investigation of domain morphology of N-Stearoylglutamic acid (N-SGA) Langmuir monolayers at the air/water interface by epifluorescence microscopy. Anisotropic feather-like domains were observed in L-enantiomeric monolayers while symmetric circular domains were found in racemic N-SGA monolayers. At a surface pressure of 30 mN/m the enantiomeric domains melted at 31 ??C while the racemic domains melted at 27 ??C. This result is exactly opposite to the behavior found in bulk crystals where the racemate melts at a higher temperature. These results were explained in terms of different molecular packing and hydrogen bonding between bulk crystals and two-dimensional thin films for enantiomeric and racemic compounds. Chapter IV summarizes the investigations of hydrogen bonding in N-acyl amino acid monolayers by vibrational sum-frequency spectroscopy (VSFS). The intermolecular hydrogen bonding interaction between the adjacent molecules through amide-amide groups in N-stearoylalanine (N-SA) is characterized by an NH stretch peak at 3311 cm-1. This is the first time that the amide NH stretching signals have been detected with the VSFS technique. A similar peak was detected at 3341 cm-1on N-SGA monolayer. The higher frequency indicates that the H-bond strength is weaker due to the larger size of the glutamic acid residue. The NH stretch mode can thus be used as a fingerprint of hydrogen bonding among amide-amide groups. A peak at 3050 cm-1 due to hydrogen bonding among carboxyl groups was also resolved from the VSFS spectra. Molecular models of intermolecular hydrogen bonding were proposed.

In this study we use AFM-based nanolithography technique to produce nanofeatures of the single strand DNA and LNA probe molecules which are prepared via thiolated nucleic acid self-assembled monolayers (SAMs) on gold substrates. The goal is to observe the topographic changes of the DNA film structures resulting from the formation of rigid double strand DNA when the target and probe DNAs bind together. The so-called hybridization depends strongly on the probe density on the substrate surface. To find the proper probe density for hybridization, we vary the concentration of the probe DNA and search for the optimal conditions for measuring the height changes of the nanofeatures. We also monitor the topographic changes of the DNA nanofeatures in the different target DNA concentrations as a function of time, and the binding isotherms are fitted with the Langmuir adsorption model to derive the equilibrium dissociation constant and maximum hybridization efficiency. In addition, we extend the nanoscale hybridization reaction detection to mismatched DNA:DNA and LNA:DNA hybridization, and observe that topographic change of mismatched hybridization is inconspicuous and rapidly reach equilibrium. The results reveal the apparent difference between the perfect match and mismatch conditions, and validate that this approach can be applied to differentiate the situations for both perfect match and mismatch cases, demonstrating its potentials in the gene chip technology.

Improving the identification ability of surfaced-immobilized nucleic acid probes for small size DNA or RNA targets, utilizing optical or electrochemical methods, has been the goal for the gene chip technology. This study focuses on new probe design for introducing hairpin structural features and locked nucleic acid modification. We use three kinds of probes (DNA-LN, DNA-HP and LNA-HP) to prepare recognition layers via self-assembly processes on a gold substrate, and utilize AFM-based nanolithography technique to produce nanofeatures to observe the stiffness changes of oligonucleotide chains resulting from the formation of rigid double stranded duplexes when target sequence hybridizes to the probe. We also monitor the topographic changes upon exposure to the single mismatched and non-complementary targets as a function of time. The results reveal LNA-HP probes exhibit the highest response to discriminating single-point mutation in the base sequence. In addition, we study the effects of salt concentration, reaction temperature and the small size on the hybridization efficiency.

In order to gain insights into the electronic interactions between metallic gold and self-assembled monolayers composed of π-conjugated thiols, a series of thiol-containing molecules based on a stilbene backbone were synthesized and assembled on gold surface. The resulted monolayers were characterized with a variety of surface-sensitive techniques and the electronic properties of the obtained surfaces were studied with the use of ultraviolet photoelectron spectroscopy. Work-function changes and alignment of the molecular energy levels with respect to the Fermi level of the metal were investigated and important insights regarding the electronic properties of the metal / organic interfaces were obtained. Another aspect of interactions between organic dyes and metallic gold was studied in the context of spectroscopic properties of systems incorporating gold nanoparticles with organic fluorophores covalently attached to the nanoparticle surface. Ultrafast dynamics of the excited-state deactivation of the organic fluorophores attached to the surface of gold nanoparticles were studied with the use of a fs transient absorption technique. It was found that the close proximity of a gold nanoparticle had a profound impact on the excited-state lifetime of the studied organic fluorophore. The influence of the structure of the studied systems on the excited-state deactivation dynamics of the organic fluorophores was described.

<p>I den här avhandlingen har vi studerat hur man kan göra nya tensider. En tensid är en speciell molekyl som har förmågan att lösa sig i både vatten och olja.</p><p>Man kan göra följande experiment hemma: Fyll en glasburk till hälften med vatten och tillsätt en droppe matolja. Oljan bildar en droppe ovanpå vattnet, därför att vatten och olja inte är blandbara. Vatten är polärt och olja är opolärt. Om man rör om med en sked kommer oljedroppen förvisso att dela upp sig i mindre droppar, men så snart man slutar att röra kommer dessa att lägga sig på vattenytan igen. Sätt nu en droppe diskmedel till blandningen och rör om. Nu sprider sig oljedropparna mycket bättre i vattnet, och de lägger sig heller inte på vattenytan lika fort när man slutar att röra. Det här beror på att diskmedel innehåller en tensid, som har en polär och en opolär del. Den polära delen passar ihop med det polära vattnet, medan den opolära delen passar ihop med den opolära oljan. På så vis kan tensiden hjälpa till att lösa upp opolära ämnen i polära vätskor.</p><p>Den aktiva delen av ett läkemedel består ofta av opolära ämnen, vilka inte löser sig i polära vätskor såsom vatten. Eftersom kroppen består till stor del av vatten måste man ändå försöka få läkemedlet vattenlösligt, för att möjliggöra transport via blodet till problemområdet. Det kan man uppnå genom att tillsätta tensider. Om läkemedel-tensidblandningen ska ges till djur eller människor får inte tensiden orsaka någon skada i kroppen.</p><p>Vi har försökt framställa tensider som ska kunna användas för att just lösa läkemedel i vatten. För att kunna framställa nya tensider måste man ha kunskap i organisk syntes. Det betyder att man måste veta hur man från små intermediat (”byggstenar”) successivt kan bygga upp nya molekyler som har de önskvärda egenskaperna. Genom olika typer av organisk syntes har vi byggt upp tre nya tensidtyper, vars egenskaper vi studerat med olika mätningar. Ingen av dessa tensider lämpade sig som tillsats till läkemedel, men vårt arbete har givit mycket ny kunskap om hur framtida tensidmolkyler kan tillverkas och vilka egenskaper de får.</p> / <p>This thesis deals with the synthesis and characterization of new polyhydroxy surfactants. The first part describes the synthesis of three new surfactant classes, and the second part concerns the surface chemical characterization of the synthesized surfactants.</p><p>A stereodivergent route for preparation of hydrophilic head groups was developed, that featured consecutive stereoselective dihydroxylations of a diene. This method provided in total four different polyhydroxylated head groups. These surfactant head groups were natural and unnatural sugar analogues, and were used for the coupling with two different hydrophobic tail groups.</p><p>Another approach took advantage of a metathesis reaction and provided a polyhydroxylated compound that was coupled to 12-hydroxy stearic acid</p><p>The third class of surfactants contained an amide linkage between the hydrophilic and the hydrophobic parts. The hydrophilic part consisted of two glucose units, and 12-hydroxy stearic acid was used as the hydrophobic part. The hydroxy moiety in the tail group was further functionalized as aliphatic esters, which provided in total four different surfactants.</p><p>A selection of the surfactants was used to investigate the chiral discrimination in Langmuir monolayers at an air-water interface. The isotherms showed a remarkable difference in compressibility between diastereomeric surfactants and also a pronounced chiral discrimination between racemic and enantiomerically pure surfactants, favoring heterochiral discrimination. The monolayers were also investigated with Brewster angle microscopy (BAM) and grazing incidence X-ray diffraction (GIXD). It was not possible to observe any chirality dependent features from the BAM images, but the GIXD measurement supported the conclusion that heterochiral discrimination governed the intermolecular forces within the racemic monolayer.</p><p>The third class of surfactants, containing an amide linkage between the glucose units and 12-hydroxy stearic acid was evaluated with respect to the CMC and the haemolytic activity. These surfactants were all haemolytic close to their respective CMC.</p>

Silicon carbide (SiC) has been around for more than 100 years as an industrial material and has found wide and varied applications because of its unique electrical and thermal properties. In recent years there has been increased attention on SiC as a viable material for biomedical applications. Among these applications are those where SiC is used as a substrate material for biosensors and biotransducers, taking advantage of its surface chemical, tribological and electrical properties. In this work we have used the proven bio- and hema-compatibility of SiC to develop a viable biorecognition interface using SiC as the substrate material for myocardial infarction detection. The approach followed included the development of an electrochemical-based sensor in which 3C-SiC is used as the active electrode and where flat band potential energy changes are monitored after successive modification of the SiC with aminopropyltriethoxysilane, anti-myoglobin and myoglobin incubation. We have studied the quality of self assembled monolayers obtained by surface modification of SiC using organosilanes such as aminopropyltriethoxysilane and octadecene, which is the starting point for the immobilization of cells or proteins on a substrate. We employed this technique on 6H-SiC where we were able to control the proliferation of H4 human neuroglioma and PC12 rat pheochromocytoma cells in vitro. Finally, aminopropyltriethoxysilane (APTES) was successfully used to immobilize anti-myoglobin on the 3C-SiC electrodes as demonstrated by fluorescence microscopy results. The electrical characterization of the surfaces was performed via impedance spectroscopy and by measuring changes in flat band potential using the Mott-Schottky plot technique. Changes in flat band and impedance of the SiC/antibody/protein interface would allow us to detect changes in the space charge region of the semiconductor. However, we believe that because of the presence of surface states and different crystal defects on the 3C-SiC we did not observed repeatable results that allowed us to identify the presence of myoglobin in solution. In addition, certain modifications need to be performed to the electrochemical cell in order to confirm the presence of the myoglobin immobilized on the functionalized SiC surfaces.

Molecular self-assembly has recently attracted significant attention for possible application in organic electronic and optoelectronic devices, such as self-assembled monolayer field-effect transistors (SAMFETs) and functional self-assembled integrated circuits. Self-assembly combines the advantages of low temperature solution processability, regio-selective monolayer adsorption and nano-scale control of film thickness. Much progress has been made in improving device performance using self-assembled monolayers (SAMs). However, most SAMFET devices reported to date showed current modulation only with submicrometre channels, with low device yields and poor reproducibility as a result of limited lateral interconnection of the semiconducting layer.In an attempt to address these issues, this thesis presents an investigation of the synthesis and properties of conjugated SAM molecules for use as the charge transporting layer in SAMFETs. Chapter 1 gives a comprehensive introduction to SAM-based surface systems, organic semiconductors and their use in OFETs and SAMFETs. Chapter 2 discusses attempts to design and synthesise p-type conjugated molecules capable of self-assembly on oxide surfaces based on a phenylene-bithiophene semiconducting core. The optical and electrochemical properties, as well as the thermal behaviour of these molecules are studied in detail. This theme is carried over to Chapter 3, which describes the synthesis, chemical and physical characterisation of two families of n-type SAM molecules. These molecules consist of NTCDI cores with hexyl or cyclohexyl chains as end-capping groups. Incorporation of a selection of materials as the active layer in OFETs or SAMFETs to evaluate the charge transport is demonstrated in Chapter 4. Monolayer films based on p-type monochlorosilane-terminated SAM molecules are made using the solution assembly technique and characterised by contact angle and AFM. OFETs made from DH-PTTP by both thermal evaporation and spin coating show high mobilities comparable to the best values reported in the literature. Top-contact SAMFETs show a hole mobility of 1.1 × 10-3 cm2V-1s-1 in air, consistent with those of solution processed DH-PTTP based OFETs. Finally, an overview of the project and some suggestions for future work are presented in Chapter 5.