Intracellular redox potential (IRP) is a measure of how oxidising or reducing the environment is within a cell. It is a function of numerous factors including redox couples, antioxidant enzymes and reactive oxygen species. Disruption of the tightly regulated redox status has been linked to the initiation and progression of cancer. However, there is very limited knowledge about the quantitative nature of the redox potential and pH gradients that exist in cancer tumour models. Multicellular tumour spheroids (MTS) are three-dimensional cell cultures that possess their own microenvironments, similar to those found in tumours. From the necrotic core to the outer proliferating layer there exist gradients of oxygen, lactate, pH and drug penetration. Tumours also have inadequate vasculature resulting in a state of hypoxia. Hypoxia is a key player in metabolic dysregulation but can also provide cells with resistance against cancer treatments, particularly chemotherapy and radiation therapy. The primary hypoxia regulators are HIFs (Hypoxia Inducible Factors) which under low O2 conditions bind a hypoxia response element, inhibiting oxidative phosphorylation and upregulating glycolysis which has two significant implications: the first is an increase in levels of NADPH/NADH, the main electron donors found in cells which impacts the redox state, whilst the second is a decrease in intracellular pH (pHi) because of increased lactate production. Thus, redox state and intracellular pHi can be used as indicators of metabolic changes within 3D cultures and provide insight into cellular response to therapy. Surface-Enhanced Raman Spectroscopy (SERS) provides a real-time, high resolution method of measuring pHi and IRP in cell culture. It allows for quick and potentially portable analysis of MTS, providing a new platform for monitoring response to drugs and therapy in an unobtrusive manner. Redox and pH-active probes functionalised to Au nanoshells were readily taken up by prostate cancer cell lines and predominantly found to localise in the cytosol. These probes were characterised by density functional theory and spectroelectrochemistry, and their in vitro behaviour modelled by the chemical induction of oxidative and reductive stress. Next, targeting nanosensors to different zones of the MTS allowed for spatial quantification of redox state and pHi throughout the structure and the ability to map the effects of drug treatments on MTS redox biology. The magnitude of the potential gradient can be quantified as free energy (ΔG) and used as a measurement of MTS viability. Treatment of PC3 MTS with staurosporine, an apoptosis inducer, was accompanied by a decrease in free energy gradients over time, whereas treatment of MTS with cisplatin, a drug to which they are resistant, showed an increase in viability indicating a compensatory mechanism and hence resistance. Finally, using this technique the effects of ionising radiation on IRP and pHi in the tumour model was explored. Following exposure to a range of doses of x-ray radiation, as well as single and multi-fractionated regimes, IRP and pHi were measured and MTS viability assessed. Increased radiation dosage diminished the potential gradient across the MTS and decreased viability. Similarly, fractionation of a single large dose was found to enhance MTS death. This novel SERS approach therefore has the potential to not only be used as a mode of drug screening and tool for drug development, but also for pre-clinical characterisation of tumours enabling clinicians to optimise radiation regimes in a patient-specific manner.

This thesis reports the investigation of spontaneous Raman Spectroscopy (RS) for its applicability in early drug discovery. A key focus has been to develop an understanding of the applicability of RS for the quantification and localisation of compound concentration inside mammalian cells. Further investigation into the use of Surface Enhanced Raman Spectroscopy (SERS) for research on Visceral Leishmaniasis (VL) and Leishmania donovani as well as investigating applicability for cancer research are decisive parts of this work. The key work described in this thesis is the investigation of whole cell concentration of compounds inside THP-1 and Madin Darby Canine Kidney (MDCK) cells. For true quantification the Cell Silent Region (CSR) is used to measure without interference from cellular background signal. The model compound is erlotinib, an anti-cancer drug with an alkyne group expressing a peak in the CSR. The developed RS system is calibrated using the current gold standard technique Ultra Performance Liquid Chromatography tandem Mass Spectrometry (UPLC-MS/MS). However, because of the single cell nature of the RS information on inter cell variability can be extracted. The RS measurements suggest that there is a large variation of concentration within single cell populations. The RS measurements can therefore give insight in single cell behaviour within a large cell population. Findings shows that washing cycles, before fixation, alter the intra-cellular concentrations significantly. This is hypothesised to be caused by the sudden change in concentration on the outside of the cell that applies an osmotic pressure, leading to loss of substance from inside the cell wall. Localisation of erlotinib is shown within THP-1 cells and points towards an accumulation inside the cell nucleus. Later, internalised Au nano-particles in the range of 30 nm to 80 nm have been investigated for their enhancement effects and localisation inside THP-1 cells. Au nano-particles are found to be internalised easily by differentiated THP-1 cells and accumulate in lysosomes. This allows for a high local enhancement of the spontaneous Raman signal. However, no advantage for the detection of lysosomally trapped compounds (chloroquine, chlorpromazine) was achieved. The detection of substances without a signal in the CSR was achieved without enhancement. Nonetheless, compounds with intrinsic peaks in the CSR could benefit from this enhancement. Lastly the RS system is explored for alternative uses in early drug discovery. This includes the detection of toxicity as well as the discrimination of cell types. Toxicity has been detected using optically trapped THP-1 cells and doxorubicin. Utilising Principal Component Analysis (PCA) combined with Linear Discriminant Analysis (LDA) on these measured spectra, allowed for a clear discrimination of toxically influenced from healthy cells. Differences mainly show up in DNA content caused by the mode of action of doxorubicin and caused by the trapping, which generates most of the signal within the nucleus of the cell. Discriminating cancerogenic (DU145) from healthy prostate cells (PNT2) has been achieved by probing fixed cells and evaluating the acquired Raman spectra with a PCA/LDA combination. The accuracy of separation of these cells when tested with a 10-fold cross-validation technique, is above 98 %, allowing a good discrimination.

ABSTRACT PREPARATION AND CHARACTERIZATION OF SILVER SERS NANOTAGS Kibar, Seda M.S., Department of Chemistry Supervisor: Prof. Dr. M&uuml / rvet Volkan December 2010, 88 pages Tags are materials used for labeling substances and so make possible the qualitative and quantitative analysis both in macroscopic and microscopic world. Nowadays, surface enhanced Raman spectroscopy became the favored one among the optical based-tag detection systems. Progress in surface enhanced Raman detection and imaging technologies depends on the availability of Raman labels with strong light scattering characteristics. In this study various SERS nanotags were prepared. An ideal SERS nanotag consists of three parts, core nanoparticle for enhancement, Raman active molecule for signature and a shell for protection and further functionalization. As a core material, silver nanoparticles were prepared using the chemical reduction method with sodium citrate as reductant. SERS enhancement provided by Ag particles prepared was examined. For colloidal stabilization and further surface modifications, silica with a controlled thickness was deposited on Ag nanoparticles. Three single-dye doped nanotags, Ag-BCB@SiO2 Ag-CFV@SiO2 and Ag-CV@SiO2 were prepared using positively charged dyes, brilliant cresyl blue (BCB), cresyl fast violet (CFV) and cresyl violet (CV). The effects of silica thickness and dye concentration in the reaction medium were examined. Stability of prepared nanotags and repeatability of the method were investigated. Multi-dye doped nanotags were prepared using BCB and CFV solutions mixed at various concentration ratios. Resulting Raman spectra Ag-BCB-CFV@SiO2 nanotags successfully exhibited characteristic peaks of each dye with a good resolution. In addition, the molar ratio between dyes BCB and CFV was reflected on the related spectra. A linear correlation was observed between the molar ratio of the dyes and their Raman intensity ratio.

Nanoscience dominates virtually every field of science and technology in the 21st century. Nanoparticles are of fundamental interest since they possess unique size- dependent properties (optical, electrical, mechanical, chemical, magnetic etc.), which are quite different from the bulk and the atomic state. Bimetallic nanoparticles are of particular interest since they combine the advantages of the individual monometallic counterparts. The present study focuses on bimetallic nanoparticles containing gold as one of the constituents. Au-Pd, Au-Pt and Au-Ag bimetallic/alloy nanoparticles have been prepared by four different synthetic methods, and characterised by a variety of techniques, with an emphasis on Au-Ag alloy systems in the solution phase as well as in the form of nanostructured films on solid substrates. Au- Ag alloy nanoparticles have been used to demonstrate two different applications. The first is the use of Au-Ag monolayer protected alloy clusters in demonstrating single electron charging events in the solution phase as well as in the dry state. Single electron transfer events involving nanosized particles are being probed extensively due to their potential applications in the field of electronics. The second is an analytical application, involving the use of trisodium citrate capped Au-Ag alloy hydrosols as substrates for surface enhanced Raman and resonance Raman scattering [SE(R)RS] studies. The sols have been used for single molecule detection purposes. Various organic molecules such as quinones, phthalocyanines and methyl violet have been self- assembled in a stepwise manner on the nanoparticulate as well as bulk Au, Ag and Au-Ag surfaces, and characterised extensively by spectroscopic, electrochemical and spectroelectrochemical techniques.

Raman spectroscopy is a promising technique because it contains abundant vibrational chemical information. However, Raman spectroscopy is restricted by its small scattering cross section, and many techniques have been developed to amplify Raman scattering intensity. In this dissertation, I study two of these techniques, coherent Raman scattering and surface enhanced Raman scattering and discuss their properties. In the first part of my dissertation, I investigate two coherent Raman processes, coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS). In CARS project, I mainly focus on the molecular resonance effect on detection sensitivity, and I find the detection sensitivity can be pushed into 10 [micromolar] with the assistance of molecular resonance. Also, I am able to retrieve background-free Raman spectra from nonresonant signals. For SRS, we develop a new SRS system by applying spectral focusing mechanism technique. We examine the feasibility and sensitivity of our SRS system. The SRS spectra of standards obtained from our system is consistent with literature, and the sensitivity of our system can achieve 10 times above shot-noise limit. In second part of this dissertation, I study surface enhanced Raman scattering (SERS) and related plasmonic effects. I synthesize different shapes of nanoparticles, including nanorod, nanodimer structure with gap and pyramids by template method, and study how electric field enhancement effects correlate to SERS by two photon luminescence (TPL). Also, I build an optical system to study optical image, spectra and particle morphology together. I find that SERS intensity distribution is inhomogeneous and closely related to nanoparticle shape and polarization direction. However, TPL and SERS are not completely correlated, and I believe different relaxation pathways of TPL and SERS and coupling of LSPR and local fields at different frequencies cause unclear correlation between them. / text

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Optical assays to detect cancer-associated molecular biomarkers in biological substrates are commonly performed with antibody-targeted organic dye contrast agents but the potential for precise quantification, long-term imaging, and multiplexed readouts is limited by chemical and optical instability, non-optimal spectral characteristics, and complicated synthetic chemistry of the dyes. This dissertation tested the hypothesis that a novel class of optical contrast agents termed polymer-protected Raman-encoded nanoparticle tags (PRENTs) provides practical advantages over existing optical technologies for molecular diagnostic applications. First, PRENTs were developed through a modular design utilizing gold-nanoparticle-Raman reporter complexes protected and functionalized by polyethylene glycol derivatives. PRENTs produced optical readouts through surface enhanced Raman scattering (SERS) that were brighter and more photostable than the fluorescence of semiconductor quantum dots under identical experimental conditions. Unique spectral signatures were produced with a broader class of Raman reporters than is possible with silica coated Raman tags. Spectral signatures and colloidal stability of PRENTs were unaffected by harsh chemical conditions that cause spectral changes and aggregation of dyes, quantum dots, and protein coated Raman tags. Antibody-targeted PRENTs specifically tagged cell surface cancer biomarkers on living cells at reasonable integration times. PRENTs were non-toxic to cells under conditions exceeding those required for sensitive molecular detection. Next, PRENTs were efficiently optimized for excitation with near-infrared light through inclusion of near-infrared chromophores as Raman reporters and exploitation of the size-dependent optical enhancement of gold nanoparticles. Third, the development of a slide-based Raman-linked immunosorbent assay using antibody-conjugated PRENTs enabled quantification of protein biomarkers with a dynamic range of 3 to 4 logs. In summary, this dissertation establishes PRENTs as novel optical tags with unique features useful for biomedical applications and provides insights for further assay development.

La diffusion Raman exaltée de surface (SERS) est utilisée pour la mise au point d’un biocapteur capable de détecter des pesticides dans l’eau, en se basant sur le suivi de l’activité enzymatique de l’Acétylcholinestérase (ACHE). Les nanoparticules d’or sont utilisées comme substrats SERS actifs. Le signal Raman exalté de l’analyte est optimisé en testant plusieurs types de nanoparticules.Le Raman SERS a permis la détection directe du Paraoxon (PO) et du carbaryl (CA) et la possibilité de suivi de l’activité de l’ACHE. En absence d'inhibiteurs, la molécule d’acétylcholine (ATC) est transformée en acide acétique et en choline par l’enzyme ACHE. La mesure de l’activité de l’ACHE repose sur le suivi des concentrations en ATC car sa transformation est inhibée en présence de pesticides. Il a été ainsi possible d’établir une relation linéaire entre la concentration de pesticides et l’exaltation du signal Raman de l’ATC non transformé. La méthode a permis la détection du PO et du CA, avec une limite de détection beaucoup plus faible que la détection directe. Ce biocapteur basé sur l’activité de l’ACHE a ensuite été utilisé pour l'évaluation d’autres polluants (inhibiteurs d’ACHE) comme les additifs contenus dans les plastiques notamment. Enfin, nous avons développé une seconde approche qui consistait à mesurer l’activité de l’ACHE en utilisant la diffusion dynamique de la lumière. En effet, nous avons montré que les paramètres physicochimiques (agrégation) des AuNPs en contact avec certaines molécules, sont fortement influencés par l’activité enzymatique de l’ACHE. C’est ce phénomène d’instabilité qui nous a permis de distinguer entre les deux cas : absence et présence de PO. / Surface-enhanced Raman scattering (SERS) was used to develop a biosensor for the detection of pesticides through the monitoring of the enzymatic activity of acetylcholinesterase (ACHE). Gold nanoparticles (AuNPs) were used as an active SERS substrate. The enhanced Raman signal of the analyte is optimized by testing several types of nanoparticles. Raman SERS allowed the direct detection of Paraoxon (PO) and carbaryl (CA) pesticides and the possibility of follow-up of the activity of the ACHE. In the absence of inhibitors, the acetylcholine (ATC) is transformed into acetic acid and choline by the enzyme ACHE. The measurement of ACHE activity is performed through the monitoring of ATC concentrations because its transformation is inhibited in the presence of pesticides. Results showed a linear correlation between the concentration of pesticides and the SERS signal of the untransformed ATC. The method was optimized for the quantification of paraoxon and carbaryl with a limit of quantification much lower than the one obtained with a direct detection. Their identification was also possible using chemometrics. This biosensors, based on the ACHE activities, was applied to the evaluation of emergent pollutants: additives of commercial polymers. Our results suggested that most of the tested polymers contained molecules that act as inhibitors of the ACHE. Finally, we propose another very simple approach to measure the ACHE activity using dynamic light scattering measurements. We found that the physicochemical parameters (aggregation) of AuNPs were strongly influenced by the enzymatic activity of ACHE when in contact with specified molecules, allowing to detect the presence of PO.

Moving towards label-free technologies is essential for many clinical and research applications. Raman spectroscopy is a powerful tool in the field of biomedicine for label-free cell characterisation and disease diagnosis, owing to its high chemical specificity. However, Raman scattering is a relatively weak process and can require long acquisition times, thus hampering its integration to clinical technologies. Multimodal analysis is currently pushing the boundaries in biomedicine, obtaining more information than would be possible using a single mode and overcoming any limitations specific to a single technique. Digital holographic microscopy (DHM) is a rapid and label-free quantitative phase imaging modality, providing complementary information to Raman spectroscopy, and is thus an ideal candidate for combination in a multimodal system. Firstly, this thesis explores the use of wavelength modulated Raman spectroscopy (WMRS), for the classification of immune cell subsets. Following this a multimodal approach, combining Raman spectroscopy and DHM, is demonstrated, where each technique is considered individually and in combination. The complementary modalities provide a wealth of information (both chemical and morphological) for cell characterisation, which is a step towards achieving a label-free technology for the identification of human immune cells. The suitability of WMRS to discriminate between closely related neuronal cell types is also explored. Furthermore optical spectroscopic techniques are useful for the analysis of food and beverages. The use of Raman and fluorescence spectroscopy to successfully discriminate between various whisky and extra-virgin olive oil brands is demonstrated, which may aid the detection of counterfeit or adulterated samples. The use of a compact Raman device is utilised, demonstrating the potential for in-field analysis. Finally, monodisperse and highly spherical nanoparticles are synthesised. A short study demonstrates the potential for these nanoparticles to benefit the techniques of surface enhanced Raman spectroscopy and optical trapping, by way of minimising variability.

Abstract Recent advances in materials synthesis resulted in a rediscovery of the low cost copper in its one and two-dimensional forms and project newer applications of this metal in fields not considered before. In this thesis, one-dimensional copper, i.e. nanowires are synthesized by a hydrothermal route and explored for their chemical, electrical, catalytic and plasmonic properties with highlighted advantages, benefited from their size and shape compared to thin film and bulk copper. Characterization of copper nanowires and their native oxides were performed using a number of analytical techniques such as X-ray photoelectron and Auger spectroscopy, Raman spectroscopy, X-ray diffraction as well as scanning probe and electron microscopy techniques to elucidate the oxidation mechanism and to assess the feasibility of the oxidized materials for various applications. A few atomic layers of cuprous oxide seem to form on the surface of the nanowires instantly, maybe already during synthesis, which then slowly grows further when exposing the nanowires to ambient air leading to the appearance of cupric oxide as well. Because of the surface oxides, individual nanowires and their bundled networks exhibit semiconducting behavior, which complicates the direct use of such materials for interconnections in electronics. However, even with the presence of native oxides, copper nanowires hold promise in many other applications such as the ones explored here for plasmonics and heterogeneous catalysis. As demonstrated in this work, surface plasmon absorption properties of the nanowires can be exploited for chemical sensing of surface adsorbed molecules (model compound Rhodamine 6G) by efficiently amplifying its Raman spectrum without using any lithographically defined sensor template. Further, it is shown that phenol contamination in water may be efficiently eliminated by converting it to nontoxic polyphenol as well as to CO2 owing to the highly efficient catalytic property of the mixed oxide phases on the surface of the nanowires. The results published in this thesis contribute to the understanding of the chemical and physical behavior of copper nanowires and other low dimensional copper nanostructures that undergo rapid surface oxidation. / Tiivistelmä Jatkuva elektronisten laitteiden ja anturien pienentäminen on hyvin linjassa teknologian kehittymisen kanssa. Pyrkimys monitoimisiin ja tehokkaisiin materiaaleihin on muuttanut tavanomaisten materiaalien käsitystä. Viimeisimmät edistysaskeleet materiaalisynteesissä ovat johtaneet edullisen kuparin uudelleenlöytämiseen sen yksi- ja kaksidimensionaalisissa muodoissa ennustaen metallille uusia sovellutuksia alueilla, joissa sitä ei ole aiemmin hyödynnetty. Tässä väitöstyössä on tutkittu hydrotermisesti syntetisoitujen yksiulotteisten kuparinanojohtimien kemiallisia, sähköisiä, katalyyttisiä ja plasmonisia ominaisuuksia sekä näiden pieneen kokoon ja muotoon perustuvia etuoja ohutkalvo- ja bulkkikupariin verrattuna. Kuparinanojohtimia ja niiden luonnollisia oksideja karakterisoitiin useilla analyysitekniikoilla kuten röntgenelektroni- ja Auger-eletronispektroskopialla, Raman-spektroskopialla, röntgendiffraktiolla sekä pyyhkäisykärki- ja elektronimikroskopialla selvittäen hapettumismekanismeja ja oksidien soveltuvuutta eri käyttötarkoituksiin. Muutaman atomikerroksen paksuinen kupari(I)oksidikerros havaittiin muodostuvan välittömästi, luultavasti jo materiaalisynteesin aikana nanojohtimien pinnalle. Nanojohtimien altistuessa ympäröivälle ilmalle oksidikerros kehittyi hitaasti johtaen kupari(II)oksidin muodostumiseen. Pintaoksidien johdosta yksittäiset nanojohtimet ja niistä yhteenkasautuneet verkostot käyttäytyvät puolijohdemaisesti mikä monimutkaistaa näiden materiaalien käyttöä sellaisenaan elektroniikan johtimissa. Luonnollisista oksideista huolimatta kuparinanojohtimet ovat lupaavia monissa muissa sovelluksissa, kuten tässä työssä tutkituissa plasmonisessa ja heterogeenisessä katalyysissä. Väitöstyössä osoitetaan, että nanojohtimen pintaplasmonisia absorptio-ominaisuuksia voidaan hyödyntää pintaan absorboituneiden molekyylien kemiallisessa havainnoinnissa (mallinnettu yhdiste rodamiini 6G) vahvistamalla Raman–spektriä käyttämättä lainkaan litografiapohjaista anturisapluunaa. Myöskin vesien fenolikontaminaatio voidaan tehokkaasti muuntaa myrkyttömiksi polyfenoleiksi ja hiiidioksidiksi hyödyntämällä nanojohtimien pinnalla olevia oksideja tehokkaana katalyyttinä (jopa parempi kuin kaupallisten kupariin pohjautuvat katalyytit). Tässä väitöstyössä julkaistut tulokset edistävät kuparinanojohtimien sekä muiden pienikokoisten ja nopeasti hapettuvien kuparinanorakenteiden kemiallisen ja fyysisen käytöksen ymmärtämistä. Tieteellisten kehitysaskeleiden lisäksi tämä väitöstyö voi myös toimia lähteenä pienirakenteisten yleisten metallien sovelluksille.