Pathogenic microbial contamination of the environment poses a significant threat to human health. Accordingly, microbial surveillance is needed to ensure safe drinking water and air quality. Current analytical methods for microbes are generally either culture-based, gene amplification-based, or sequencing-based. However, these approaches require centralized facilities, well-trained personnel, and specialized instruments that result in high costs and long turnaround times. Surface-enhanced Raman spectroscopy (SERS)-based techniques have been proposed to overcome these limitations. In this dissertation, we discuss work conducted to develop novel SERS-based methods to enable both sensitive microbial quantification and analysis of the interactions of pathogens, their hosts, and the surrounding environment. We first developed a labeled SERS-based lateral flow test for virus quantification. Optimization of the lateral flow design and digital signal analysis enabled high sensitivity towards SARS-CoV-2. To elicit a comprehensive understanding of pathogen infection, label-free living-cell SERS sensors were engineered by incubating host cells with nanoparticles. SERS spectral changes in host cellular components and metabolites during infection were used for viral quantification and offered inherent insights into the temporal and spatial molecular-level mechanisms of infection. These biosensors were validated using bacteriophage Phi6 and then developed for infectious H1N1 influenza. To understand microbial survival in the environment, living-cell SERS methods were applied under various conditions. Results showed cell inactivation and antibiotic treatment induced significant cellular and metabolic responses in the living whole-cell sensors, implying their potential applicability to various environmental conditions. Our research achieves rapid and on-site pathogen quantification and infection mechanism identification. / Doctor of Philosophy / Pathogenic microbes, such as the SARS-CoV-2 virus, can spread through air and water and are potentially harmful to human health. Monitoring the concentrations of these microbes in the environment is crucial to track their presence and provide an early warning of their spread. Unfortunately, current microbial detection methods are often expensive and take a long time since they typically require professional facilities and expert elicitation. Our research relies on a technique called surface-enhanced Raman spectroscopy (SERS) to address these challenges. SERS enables identification and quantification of microbes by analyzing specific features (i.e., peak position, peak intensity) in the spectra. We first applied this technique by modifying a commercial SARS-CoV-2 antigen test kit with a label molecule that provides SERS signals. We achieve accurate and sensitive quantification, even in the presence of high levels of environmental interference. To better understand how these harmful microbes interact with our bodies, we developed sensors that can measure SERS signal changes in host cells before and after infection. These sensors were tested using the bacteriophage virus Phi6 that infects bacteria and infectious H1N1 influenza virus. Furthermore, we applied these sensors to study how bacteria respond to different environmental conditions, providing valuable insights into their survival and behavior under various conditions. In summary, our research introduces methods that are more accessible to identify and quantify harmful microbes that can be potentially used by the general public. The methods provide us with molecular level understanding of pathogen interactions with humans and the environment.

Raman optical activity (ROA) is a powerful probe of the structure and behaviour of biomolecules in aqueous solution for a number of important problems in molecular biology. Although ROA is a very sensitive technique for studying biological samples, it is a very weak effect and the conditions of high concentration and long data collection time required limit its application for a wide range of biological samples. These limitations could possibly be overcome using the principle of surface enhanced Raman scattering (SERS). The combination of ROA with SERS in the form of surface enhanced ROA (SEROA) could be a solution for widening the application of ROA. In the last few years, the generation of reliable SEROA spectra of biomolecules has been problematic due to non-homogenous colloidal systems forming and low signal-to-noise ratios which complicated detection of the true SEROA signal from the analyte. L- and D-enantiomers give full or partially mirror image chiroptical spectra, this property of enantiomers can be employed to prove the chiroptical activity of the SEROA technique. In this thesis we employed a hydrophilic polycarbopol polymer as stabilising media which has led to the first report of mirror image SEROA bands for enantiomeric structures. This new technique of incorporating the hydrogel polymer as a means to stabilise the colloidal system has proven to be reliable in obtaining high quality SEROA spectra of D- and L-enantiomers of ribose and tryptophan. In an extension of the hydrogel-stabilised SEROA work, we also demonstrate that single nanoparticle plasmonic substrate such as silver silica nanotags can enhance the weak ROA effect. These dye tagged silica coated silver nanoparticles have enabled a chiral response to be transmitted from a chiral analyte to the plasmon resonance of an achiral metallic nanostructure. The measurement of mirror image SERROA bands for the two enantiomers of each of ribose and tryptophan was confirmed for this system. The generation of SEROA for both systems was achieved and confirmed SEROA as a new sensitive tool for analysis of biomolecular structure. In a related project, Raman and ROA spectra were measured for adenosine and seven of its derivative ribonucleotides. Both of these spectroscopic techniques are shown to be sensitive to the site and degree of phosphorylation, with a considerable number of marker bands being identified for these ribonucleotides. Moreover, the SERS studies of these ribonucleotides were also performed. The obtained SERS spectra were shown similar features that confirm these analytes interact with the surface in a similar manner, hence limiting the structural sensitivity of this method towards phosphate position. Short dipeptides such as diketopiperazine (DKP) have been investigated during the last decades as both natural and synthetic DKPs have a wide variety of biological activities. Raman and ROA spectra of linear and cyclic dialanine and diserine were measured to charecterize their solution structures. Density functional theory (DFT) calculations were carried out by a collaborator to assist in making vibrational band assignments. Considerable differences were observed between the ROA bands for the cyclic and linear forms of both dialanine and diserine that reflect large differences in the vibrational modes of the polypeptide backbone upon cyclicization. In this study, the ROA spectra of cyclic dialanine and diserine have been reported for the first time which demonstrated that ROA spectroscopy when utilised in combination with computational modelling clearly provides a potential tool for characterization of cyclic peptides.

Many biological processes, pathogens, and pharmaceuticals act upon, cellular membranes. Accordingly, cell membrane mimics are attractive targets for biosensing, with research, pathology, and pharmacology applications. Lipid bilayers represent a versatile sensor functionalization platform providing antifouling properties, and many receptor integration options, uniquely including transmembrane proteins. Bilayer-coated sensors enable the kinetic characterization of membrane/analyte interactions. Addressed theoretically and experimentally is the self-assembly of model membranes on plasmonic sensors. Two categories of plasmonic sensors are studied in two parts. Part I aims to deposit raft-forming bilayers on planar nanoaperture arrays suitable for multiplexing and device integration. By vesicle fusion, planar bilayers are self-assembled on thiol-acid modified flame-annealed gold without the need for specific lipid head-group requirements. Identification of coexisting lipid phases is accomplished by AFM imaging and force spectroscopy mapping. These methods are successfully extended to metallic, plasmon-active nanohole arrays, nanoslit arrays and annular aperture arrays, with coexisting phases observed among the holes. Vis-NIR transmission spectra of the arrays are measured before and after deposition, indicating bilayer detection. Finally, the extraction of membrane proteins from cell cultures and incorporation into model supported bilayers is demonstrated. These natural membrane proteins potentially act as lipid-bound surface receptors. Part II aims to encapsulate in model lipid bilayers, metallic nanoparticles, which are used as probes in surface enhanced Raman spectroscopy. Three strategies of encapsulating particles, and incorporating Raman-active dyes are demonstrated, each using a different dye: malachite green, rhodamine-PE, and Tryptophan. Dye incorporation is verified by SERS and the bilayer is visualized and measured by TEM, with support from DLS and UV-Vis spectroscopy. In both parts, lipid-coated sensors are successfully fabricated and characterized. These results represent important and novel solutions to the functionalization of plasmonic surfaces with biologically relevant cell membrane mimics.

Plasmonics techniques, such as surface plasmon resonance (SPR) and surface-enhanced Raman scattering (SERS), have been widely used for chemical and biochemical sensing applications. One approach to excite surface plasmons is through the coupling of light into metallic grating nanostructures. Those grating nanostructures can be fabricated using state-of-the-art nanofabrication methods. Laser interference lithography (LIL) is one of those methods that allow the rapid fabrication of nanostructures with a high-throughput. In this thesis, LIL was combined with other microfabrication techniques, such as photolithography and template stripping, to fabricate different types of plasmonic sensors. Firstly, template stripping was applied to transfer LIL-fabricated patterns of one-dimensional nanogratings onto planar supports (e.g., glass slides and plane-cut optical fiber tips). A thin adhesive layer of epoxy resin was used to facilitate the transfer. The UV-Vis spectroscopic response of the nanogratings supported on glass slides demonstrated a strong dependency on the polarization of the incident light. The bulk refractive index sensitivities of the glass-supported nanogratings were dependent on the type of metal (Ag or Au) and the thickness of the metal film. The described methodology provided an efficient low-cost fabrication alternative to produce metallic nanostructures for plasmonic chemical sensing applications. Secondly, we demonstrated a versatile procedure (LIL either alone or combined with traditional laser photolithography) to prepare both large area (i.e. one inch2) and microarrays (μarrays) of metallic gratings structures capable of supporting SPR excitation (and SERS). The fabrication procedure was simple, high-throughput, and reproducible, with less than 5 % array-to-array variations in geometrical properties. The nanostructured gold μarrays were integrated on a chip for SERS detection of ppm-level of 8-quinolinol, an emerging water-borne pharmaceutical contaminant. Lastly, the LIL-fabricated large area nanogratings have been applied for SERS detection of the mixtures of quinolone antibiotics, enrofloxacin, an approved veterinary antibiotic, and one of its active metabolite, ciprofloxacin. The quantification of these analytes (enrofloxacin and ciprofloxacin) in aqueous mixtures were achieved by employing chemometric analysis. The limit of quantification of the method described in this work is in the ppm-level, with <10 % SERS spatial variation. Isotope-edited internal calibration method was attempted to improve the accuracy and reproducibility of the SERS methodology. / Graduate / 2018-02-17

G-quadruplexes (G4s) are nucleic acid structures formed from π-stacked planar sets of four Hoogsteen hydrogen bonded guanine bases. G4s emerged as potential therapeutic targets based on their ability to modulate gene expression and inhibit the ability of telomerase to elongate chromosomal telomeres. Raman spectroscopy, polarized Raman spectroscopy, surface-enhanced Raman spectroscopy (SERS), and other optical spectroscopic techniques were used to characterize the G4s formed by four different DNA sequences: human telomeric (HT), thrombin-binding aptamer (TBA), nuclease hypersensitive element III1 region of the c- Myc gene promoter (Myc), and a single loop-isomer of Myc (MycL1). / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2015. / FAU Electronic Theses and Dissertations Collection

Corantes orgânicos são uma importante classe de poluentes ambientais, sendo que a natureza da interação de tais espécies com ácidos húmicos determina seu comportamento e destino ambiental. Este trabalho investiga abordagens diferentes para a síntese de nanopartículas de ouro-ácido húmico (NPs Au/AH), o desempenho destas partículas como sensores para a determinação de traço de corantes orgânicos e da natureza da sua interação química com ácidos húmicos por técnicas de espectroscopia Raman intensificada por superfície (surface-enhanced Raman scattering, SERS). As nanopartículas de ouro foram obtidas de forma direta em meio aquoso. A síntese foi realizada na presença de ácido húmico em vários valores de pH e na presença e na ausência de citrato de sódio. Nesta abordagem, o ácido húmico apresenta propósitos diferentes. Na síntese das nanopartículas, ele serve como agente redutor e para a estabilização da superfície, impedindo a coalescência das nanopartículas em meio aquoso. Considerando-se a utilização de nanopartículas como substratos SERS-ativos, o ácido húmico serve como uma fase de extração associada com a plataforma SERS, favorecendo a interação dos corantes orgânicos com as nanopartículas metálicas. Esta abordagem pode ser utilizada para aumentar a sensibilidade e seletividade da técnica SERS e evitar a interferência de outras espécies em solução. É também importante mencionar que o ácido húmico dá origem a um espectro Raman muito fraco e, portanto, não interfere de forma significativa na detecção espectroscópica das espécies de interesse. As NPs Au/AH obtidas foram caracterizadas por espectroscopia eletrônica, microscopia eletrônica de varredura e SERS, a fim de estabelecer uma correlação entre a sua morfologia, plasmon superficial, e seu uso potencial como substratos SERS. As NPs Au/AH foram utilizadas como substratos SERS no estudo de corantes têxteis aniônicos e catiônicos. Os espectros Raman, nestes casos, foram atribuídos ao complexo formado pelo ácido húmico e cada uma das espécies de interesse. Os resultados obtidos revelaram uma dependência significativa entre as propriedades morfológicas e eletrônicas das NPs Au/AH com o procedimento de síntese, e também uma interação preferencial entre as nanopartículas e os corantes catiônicos. Conclui-se que as NPs Au/AH podem proporcionar uma abordagem útil para a caracterização espectroscópica de espécies relevantes para o ambiente e sua interação química com os ácidos húmicos, através do uso da espectroscopia Raman intensificada pela superfície / Organic dyes are an important class on environmental pollutants, and the nature of the interaction of such species with humic acid strongly determines their environmental behavior and fate. This work investigates different approaches for the synthesis of humic acid-gold nanoparticles (HA-AuNP), the performance of these particles as sensors for trace determination of organic dyes and the nature of their chemical interaction with humic acids by surface-enhanced Raman scattering (SERS). The Au nanoparticles were obtained by direct fabrication in aqueous media.The synthesis were carried out in the presence of humic acid at various pH values, and in the presence and absence of sodium citrate. In this approach, humic acid serves different purposes. In the synthesis of the nanoparticles, they serve as reducing agent and for surface stabilization, preventing coalescence of the nanoparticles in aqueous media. Considering the use of the nanoparticles as SERSactive substrates, the humic acid serves as an extraction phase associated with the SERS platform, favoring the interaction of the organic dyes with the metallic nanoparticles. This approach can be used to enhance the sensitivity and selectivity of SERS technique and avoid interference from other species in solution. It is also important to mention that the humic acid gives rise to a very weak Raman spectrum, and therefore does not interfere significantly in the spectroscopic detection of the species of interest. The obtained HA-AuNPs were characterized by electronic spectroscopy, scanning electron microscopy and SERS, in order to establish a correlation between their morphology, surface plasmon, and their potential use as SERS platforms. The HA-AuNPs have been applied as SERS substrates for anionic and cationic textile dyes. The recorded Raman spectra are, in these cases, assigned to the complex formed by the humic acid and each of the species of interest. The obtained results revealed a significant dependence on the morphological and electronic properties of the HA-AuNPs with the synthesis procedure, and also a strong interaction between the nanoparticles and cationic dies. We conclude that HA-AuNP may provide a valuable approach for the spectroscopic characterization of environmentally relevant species and their chemical interaction with humic acids, through the use of surface enhanced Raman spectroscopy

Corantes orgânicos são uma importante classe de poluentes ambientais, sendo que a natureza da interação de tais espécies com ácidos húmicos determina seu comportamento e destino ambiental. Este trabalho investiga abordagens diferentes para a síntese de nanopartículas de ouro-ácido húmico (NPs Au/AH), o desempenho destas partículas como sensores para a determinação de traço de corantes orgânicos e da natureza da sua interação química com ácidos húmicos por técnicas de espectroscopia Raman intensificada por superfície (surface-enhanced Raman scattering, SERS). As nanopartículas de ouro foram obtidas de forma direta em meio aquoso. A síntese foi realizada na presença de ácido húmico em vários valores de pH e na presença e na ausência de citrato de sódio. Nesta abordagem, o ácido húmico apresenta propósitos diferentes. Na síntese das nanopartículas, ele serve como agente redutor e para a estabilização da superfície, impedindo a coalescência das nanopartículas em meio aquoso. Considerando-se a utilização de nanopartículas como substratos SERS-ativos, o ácido húmico serve como uma fase de extração associada com a plataforma SERS, favorecendo a interação dos corantes orgânicos com as nanopartículas metálicas. Esta abordagem pode ser utilizada para aumentar a sensibilidade e seletividade da técnica SERS e evitar a interferência de outras espécies em solução. É também importante mencionar que o ácido húmico dá origem a um espectro Raman muito fraco e, portanto, não interfere de forma significativa na detecção espectroscópica das espécies de interesse. As NPs Au/AH obtidas foram caracterizadas por espectroscopia eletrônica, microscopia eletrônica de varredura e SERS, a fim de estabelecer uma correlação entre a sua morfologia, plasmon superficial, e seu uso potencial como substratos SERS. As NPs Au/AH foram utilizadas como substratos SERS no estudo de corantes têxteis aniônicos e catiônicos. Os espectros Raman, nestes casos, foram atribuídos ao complexo formado pelo ácido húmico e cada uma das espécies de interesse. Os resultados obtidos revelaram uma dependência significativa entre as propriedades morfológicas e eletrônicas das NPs Au/AH com o procedimento de síntese, e também uma interação preferencial entre as nanopartículas e os corantes catiônicos. Conclui-se que as NPs Au/AH podem proporcionar uma abordagem útil para a caracterização espectroscópica de espécies relevantes para o ambiente e sua interação química com os ácidos húmicos, através do uso da espectroscopia Raman intensificada pela superfície / Organic dyes are an important class on environmental pollutants, and the nature of the interaction of such species with humic acid strongly determines their environmental behavior and fate. This work investigates different approaches for the synthesis of humic acid-gold nanoparticles (HA-AuNP), the performance of these particles as sensors for trace determination of organic dyes and the nature of their chemical interaction with humic acids by surface-enhanced Raman scattering (SERS). The Au nanoparticles were obtained by direct fabrication in aqueous media.The synthesis were carried out in the presence of humic acid at various pH values, and in the presence and absence of sodium citrate. In this approach, humic acid serves different purposes. In the synthesis of the nanoparticles, they serve as reducing agent and for surface stabilization, preventing coalescence of the nanoparticles in aqueous media. Considering the use of the nanoparticles as SERSactive substrates, the humic acid serves as an extraction phase associated with the SERS platform, favoring the interaction of the organic dyes with the metallic nanoparticles. This approach can be used to enhance the sensitivity and selectivity of SERS technique and avoid interference from other species in solution. It is also important to mention that the humic acid gives rise to a very weak Raman spectrum, and therefore does not interfere significantly in the spectroscopic detection of the species of interest. The obtained HA-AuNPs were characterized by electronic spectroscopy, scanning electron microscopy and SERS, in order to establish a correlation between their morphology, surface plasmon, and their potential use as SERS platforms. The HA-AuNPs have been applied as SERS substrates for anionic and cationic textile dyes. The recorded Raman spectra are, in these cases, assigned to the complex formed by the humic acid and each of the species of interest. The obtained results revealed a significant dependence on the morphological and electronic properties of the HA-AuNPs with the synthesis procedure, and also a strong interaction between the nanoparticles and cationic dies. We conclude that HA-AuNP may provide a valuable approach for the spectroscopic characterization of environmentally relevant species and their chemical interaction with humic acids, through the use of surface enhanced Raman spectroscopy

In the pursuit of economical and rapid fabrication solutions on the micro and nano scale, polymer replication has proven itself to be a formidable technique, which despite zealous development by the research community, remains full of promise. This thesis explores the potential of elastomers in what is a distinctly multidisciplinary field. The focus is on developing innovative fabrication solutions for planar photonic devices and for nanoscale devices in general. Innovations are derived from treatments of master structures, imprintable substrates and device applications. Major contributions made by this work include fully replicated planar integrated optical devices, nanoscale applications for photolithographic standing wave corrugations (SWC), and a biologically templated, optical fiber based, surface-enhanced Raman scattering (SERS) sensor. The planar devices take the form of dielectric rib waveguides which for the first time, have been integrated with long-period gratings by replication. The heretofore unemployed SWC is used to demonstrate two innovations. The first is a novel demonstration of elastomeric sidewall photolithographic mask, which exploits the capacity of elastomers to cast undercut structures. The second demonstrates that the corrugations themselves in the absence of elastomers, can be employed as shadow masks in a directional flux to produce vertical stacks of straight lines and circles of nanowires and nanoribbons. The thesis then closes by conceptually combining the preceding demonstrations of waveguides and nanostructures. An optical fiber endface is em ployed for the first time as a substrate for patterning by replication, wherein the pattern is a nanostructure derived from a biological template. This replicated nanostructure is used to impart a SERS capability to the optical fiber, demonstrating an ultra-sensitive, integrated photonic device realized at great economy of both time and money, with very real potential for mass fabrication.

The interaction between nanoscience and biomedicine is one of the important developing areas of modern science. The usage of functional nanoparticles with biological molecules provides sensitive and selective detection, labeling and sensing of biomolecules. Until today, several novel types of tagging materials have been used in bioassays, such as plasmon-resonant particles, quantum dots (QDs), and metal nanoshells. However, nowadays, Surface enhanced raman scattering (SERS) tags have been attracting considerable attention as a tagging system. SERS-tags provide high signal enhancement, and they enable multiplex detection of biomolecules due to high specificity. This thesis is focused on the designing proper SERS nanotags for DNA studies. SERS nano-tags are nanostructures consisting of core nanoparticle generally silver, Raman reporter molecule for labeling, and shell to make surface modifications and to prevent deterioration arising from environmental impact. Based on this information, silver core synthesized by thermal decomposition and chemical reduction methods. Thermal decomposition method provides synthesis of silver nanoparticles in hydrophobic medium, resulting in proper silica coating by reverse microemulsion method. On the other hand, silver nanoparticles sythesized by chemical reduction method exhibit hydrophilic property. Due to capping reagents, negatively charged silver nanoparticles could easily attach with positively charged Raman dye which is brilliant cresyl blue (BCB). After addition of Raman active molecule, silica coating process was done by using modified St&ouml / ber method. The resulting particles were characterized by Scanning Electron Microscopy (SEM), Energy-dispersive X-ray spectroscopy (EDX) ,UV-vis Spectrometry (UV-vis) and Surface-Enhanced Raman Spectroscopy (SERS). In recent years, DNA detection has gained importance for cancer and disease diagnosis and the detection of harmful microorganisms in food and drink. In this study, gene sequences were detected via SERS. For this, probe sequences were labelled with Raman reporter molecule, BCB,and SERS nano-tags and were called as SERGen probes. Then, after hybridization of DNA targets to complementary probe sequences onto gold substrate, SERS peak was followed.

Metal nanostructures exhibit a wide variety of interesting physical and chemical properties, which can be tailored by altering their size, morphology, composition, and environment. Gold and silver nanostructures have received considerable attention for many decades because of their widespread use in applications such as catalysis, photonics, electronics, optoelectronics, information storage, chemical and biological sensing, surface plasmon resonance and surface-enhanced Raman scattering (SERS) detection. This thesis is composed of three main parts about the synthesis, characterization and SERS applications of shape-controlled and surface modified noble metal nanoparticles. The first part is related to a simple synthesis of shape controlled solid gold, hollow gold, silver, gold-silver core-shell, hollow gold-silver double-shell nanoparticles by applying aqueous solution chemistry. Nanoparticles obtained were used for SERS detection of dye molecules like brilliant cresyl blue (BCB) and crystal violet (CV) in aqueous system. v The second part involves the synthesis of surface modified silver nanoparticles for the detection of dopamine (DA) molecules. Determination of a dopamine molecule attached to a iron-nitrilotriaceticacid modified silver (Ag-Fe(NTA)) nanoparticles by using surface-enhanced resonance Raman scattering (SERRS) was achieved. The Ag-Fe (NTA) substrate provided reproducibility and excellent sensitivity. Experimental results showed that DA was detected quickly and accurately without any pretreatment in nM levels with excellent discrimination against ascorbic acid (AA) (which was among the lowest value reported in direct SERS detection of DA). In the third part, a lanthanide series ion (Eu3+) containing silver nanoparticle was prepared for constructing a molecular recognition SERS substrate for the first time. The procedure reported herein, provides a simple way of achieving reproducible and sensitive SERS spectroscopy for organophosphates (OPP) detection. The sensing of the target species was confirmed by the appearance of an intense SERS signal of the methyl phosphonic acid (MPA), a model compound for nonvolatile organophosphate nerve agents, which bound to the surface of the Ag-Eu3+ nanostructure. The simplicity and low cost of the overall process makes this procedure a potential candidate for analytical control processes of nerve agents.