Richmond Ltd. has recently undergone a change in strategy, away from the traditional commodity based meat industry, towards the modern food business. To do this, opportunities to add value to their current product range must be identified. This involves the conversion of traditionally low value commodity based products into products that demand a premium. An example of this is converting muscles that are currently used for grinding meat into a further processed convenience food (i.e. ready meals). Another method is to add further value to premium products by making them more appealing to consumers (i.e. nutritional information on labels). This work details investigations into the functional properties of selected beef forequarter muscles (low value commodity products) and the nutritional properties of selected export lamb products (premium products). The functional properties of a number of beef forequarter muscles were measured to identify which had the best potential for further processing applications with respect to ready meals. The functional properties of tenderness, cook loss and shrinkage were measured for the Latissimus Dorsi, Pectorialis Profundus (Point End Brisket), Infraspinatus (Cross Cut Blade), Triceps Brachi Longhead (Main muscle in Bolar Shoulder Clod), Supraspinatus (Chuck Tender), Serratus Ventralis and Triceps Brachi Medialhead (Muscle in Bolar Shoulder Clod. From the tests conducted the Infraspinatus and the Triceps Brachi Longhead have been identified as having the best functional properties with respect to further processing for ready meal applications. As well as conducting tests to identify the forequarter muscles with the best potential for further processing applications, investigations were carried out to identify cooking regimes that would optimise the functional properties. This work confirmed that there are three major chemical reactions, which determine the resultant functional properties of cooked meat. They are the denaturation and aggregation of the myofibrillar proteins and the denaturation and solubilisation of connective tissue (collagen). At around 50°C myosin (45% to 50% of the myofibrillar proteins) denatures, which results in a substantial increase in cook loss and reduction in water holding capacity. At around 60°C collagen (main connective tissue protein) denatures, which results in a substantial increase in tenderness and increase in cook loss. This is because as the collagen denatures it loses it mechanical strength (increase in tenderness) and can no longer support its own structure, and causes it to contract. This contraction causes fluid within the meat and cook loss caused by the denaturation of myosin to be expelled from the meat by compressive forces (squeezed out). At around 70°C actomyosin (22% of the myofibrillar proteins) denatures. This results in a substantial increase in the cook loss and firming of the meat. The increase in cook loss or decrease in water holding capacity that occurs with myofibrillar protein denaturation is due to the fact that when these proteins denature and aggregate their ability to bind water is greatly reduced. From the results of the cooking regime trials it is recommended that for functional property considerations that during the cooking of further processed meat products (i.e. ready meal applications) a meat temperature of 62°C should be aimed for, for the slowest heating region during cooking (usually the centre). This is because it has been identified that a cooking temperature of 65°C should not be exceeded otherwise detrimental effects can occur to the functional properties of the cooked meat. For health concerns a 7D bacterial death reduction has to be achieved. This means that for a cooking temperature of 62°C the meat has to be held at this temperature for at least 5 minutes. Therefore the total cooking time would be the time needed to heat all the meat to 62°C plus 5 minutes to ensure a safe product. The heating or cooking system employed should also ensure that a minimal amount of the meat is heated above 65°C. This can be easily achieved by minimising the external cooking temperature, but long cooking times will result. An industrial cooking process will be a compromise between the cost associated with longer residence time and product functionality. As mentioned earlier another way to add value is to supply nutritional information for selected cuts. Consequentially one of the objectives of this project was to provide some nutritional information for selected meat cuts. Though the primary objective of this part of the project was to develop a method for producing the needed information, so that Richmond N.Z. Ltd. can develop further information on an as needs basis. The nutritional characteristics of a number of export lamb cuts from the saddle region has also been investigated and a method devised to allow further characterisation of other cuts. The method involves breaking down a standard cut into its constituent components (e.g. Frenched rack consists of loin eye, fat cap, intercostals and fatty tissue). The constituent components are tested for their nutritional properties. The frenched rack nutritional properties are calculated from the nutritional properties of the constituents components and the yield data (percentage of each constituent component within a frenched rack) for frenched racks. This method allowed the identification of the main sources of variation for nutritional characteristics. These differences were found to be caused by the lean to fat ratio, not nutritional differences in lean tissue from the same region of lamb (i.e. loin eye and tenderloin very similar nutritionally). The difference in lean to fat ration also accounts for the variation between grades (i.e. PX grade lamb cuts have a higher fat content than YX grade lamb cuts due to PX grade cuts having a higher percentage fat tissue in their cuts). The cuts characterised were the shortloin section (whole section or chop), rack section (whole section or chop), 75mm racks frenched 25mm, boneless loin and tenderloin for both PX and YX grade lamb. The method will be applicable to other regions of lamb (i.e. hindquarter and forequarter) for which nutritional information already exists, but for which yielding data will have to be collected. The method would also be applicable to other species such as beef and venison, but both nutritional data for constituent components and yielding data would have to be collected.

Orientadores: Rosiane Lopes da Cunha, Miriam Dupas Hubinger / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-10T19:31:23Z (GMT). No. of bitstreams: 1 Neves_EdmeiaSabadini_D.pdf: 3460318 bytes, checksum: 852074cc798cd99ff46cf910e7887c71 (MD5) Previous issue date: 2008 / Resumo: Foram estudadas as interações entre as proteínas do leite e a carragena em sistemas acidificados com glucona-delta-lactona (GDL) contendo ou não co-solutos, como açúcar (sacarose) e a mistura salina KCl/NaCl, na formação/obtenção de géis. Foi possível avaliar o efeito das variáveis de composição (concentrações de caseinato de sódio, concentrado protéico do soro, carragena, sacarose ou mistura salina KCl/NaCl) e condições de processo (temperatura de mistura dos componentes, tempo de aquecimento e velocidade de agitação) nas propriedades mecânicas e da capacidade de retenção de água dos géis protéicos acidificados, utilizando a metodologia de planejamento experimental fatorial. Essas análises foram complementadas com microscopia eletrônica de varredura e calorimetria diferencial de varredura. Nos géis obtidos com adição de sacarose verificou-se que a concentração de carragena foi a variável de maior contribuição ao aumento da dureza, deformabilidade e firmeza dos géis. Através dos ensaios de relaxação de tensões, verificou-se que o módulo elástico foi fortemente influenciado pelas interações entre a carragena e o caseinato de sódio, na presença do açúcar. O gel mais forte foi obtido em altas concentrações de biopolímeros, sendo o efeito da sacarose associado à diminuição das interações polissacarídeo-solvente. Na análise dos ensaios de ruptura e de relaxação de tensões constatou-se que os géis com a adição da mistura salina (KCl/NaCl), comportaram-se de maneira diferente dos com e sem sacarose. Foram estruturalmente muito mais frágeis e, em certas formulações, não se formou gel, sendo a força iônica e a temperatura de processo, as variáveis que definiram as características reológicas do sistema com sal. Pode-se observar o efeito negativo da concentração do concentrado protéico do soro (CPS) nas propriedades mecânicas do gel lácteo. Na avaliação da capacidade de retenção de água nos sistemas contendo sal, o comportamento foi totalmente diferente do da sacarose. A adição do açúcar promoveu o fortalecimento da rede do gel, com uma malha mais firme e coesa ao contrário do observado para os géis com adição da mistura salina KCL/NaCl / Abstract: Gel formation due to interactions between milk proteins and carrageenan in systems acidified by glucono-delta-lactona (GDL) with or without co-solutes like sugar (sucrose) and KCl/NaCl, were studied. A factorial experimental design was used to determine the effect of several variables, such as: the composition of the system (concentrations of sodium caseinate, whey protein concentrate, carrageenan and sucrose or a KCl/NaCl mixture); the process conditions (temperature of the mixture, heating time and stirring speed), on the mechanical properties of the acidified gels, as well as their water holding capacity. Scanning Electronic Microscopy and Differential Scanning Calorimetry were also used to complement the studies. In the gels containing sucrose, the concentration of carrageen was the more important variable with respect to the increase in hardness, rigidity and consistence of the gels. Using the stress relaxation experiments, it was observed that the elastic modulus was highly affected by the interactions between the carrageenan and sodium caseinate if sucrose was present. The strongest gel was obtained with the higher concentrations of the biopolymers, and this can be attributed to a decrease in the interactions between the polysaccharides and the water. In the presence of salts (KCl/NaCl) the stress relaxation and rupture experiments showed that the gels obtained were different from those obtained with the addition of sucrose or without a solute. The gels containing salts were much weaker and in some cases failed to form a gel. For these gels, the ionic strength and the temperature were the more important variables affecting the rheological properties of the gels. On the other hand, a negative effect of the concentration of whey protein concentrate on the mechanical properties of the lacteous gels could also be observed, due to strong interactions between the sodium caseinate and carrageenan. In terms of the water holding capacity, the behaviors of the gels containing salts and sucrose were again completely different. In the presence of sucrose, the molecular structure of the gel became stronger and cohesive, the opposite effect being observed in gels containing salts (KCl/NaCl) / Doutorado / Doutor em Engenharia de Alimentos

L'amélioration de la qualité nutritionnelle des produits carnés cuits nécessite une meilleure compréhension des changements physicochimiques des protéines induits au chauffage. Ce travail porte sur l'analyse des mécanismes à l'origine des changements d'état des protéines afin de développer un modèle stoechio-cinétique de prédiction de l'effet de la composition et de la température sur ces changements. Un modèle expérimental, représentant l'environnement physicochimique du tissu musculaire (pH et force ionique), a permis de quantifier l'incidence spécifique de la chaleur, de la composition en fibres, en oxydants (fer, peroxyde d'hydrogène et vitamine C) et en antioxydants (enzymatiques, vitaminique et peptidique) sur l'oxydation, la dénaturation thermique et l'agrégation des protéines. Le modèle stoechio-cinétique est constitué de 43 réactions, représentant l'ensemble des phénomènes mis en jeu dans le modèle expérimental : chimie de Fenton, attaques radicalaires des acides aminés et dénaturation thermique. La résolution du système d'équations différentielles permet de calculer les concentrations des composés au cours du chauffage ; 3 constantes de vitesse inconnues ont été ajustées à partir des cinétiques expérimentales. Les résultats expérimentaux montrent : (1) un effet synergique des oxydants et du chauffage sur les oxydations, (2) une incidence négligeable des oxydants sur la dénaturation thermique et l'agrégation, (3) une sensibilité accrue des protéines de fibres α-white aux oxydations et à la dénaturation thermique par rapport à celles de fibres β-red et (4) un important effet de la nature des oxydants et des antioxydants sur les taux d'oxydation. Les prédictions du modèle stoechio-cinétique permettent de reproduire les tendances expérimentales. En partant de cette base, les modèles expérimentaux et mathématiques pourront être complexifiés progressivement pour avoir un outil prédictif de la qualité nutritionnelle des viandes cuites. / Improving the nutritional quality of cooked meat products needs a better understanding of protein physicochemical changes induced by heating. This study aims to analyse the mechanisms responsible to protein state changes, in the goal to develop a predictive stoichio-kinetic model of effect of composition and temperature on these changes. An experimental model which represent the physicochemical environment of meat tissue (pH and ionic strength) allowed to quantify the specific effect of heating, composition in fibres, in oxidants (iron, hydrogen peroxide and vitamin C) and in antioxidants (enzymes, vitamins and peptides) on oxidations, thermal denaturation (hydrophobicity) and aggregation of proteins. The stoichio-kinetic model is composed of 43 reactions which represent all phenomenon involved in the experimental model : Fenton chemistry, radical attack on amino acids and thermal denaturation. A system of differential equation solver allows to determine the concentration of compounds during heating ; 3 unknown rate constants were adjusted with experimental kinetics. Experimental results show : (1) a synergistic effect of oxidants and heating on protein oxidation, (2) a negligible impact of oxidants on thermal denaturation and aggregation (3) a significant higher sensitivity to oxidation and thermal denaturation of protein from α-white than those from β-red, (4) an important effect of the composition in oxidants and antioxidants on the protein oxidation levels. Stoichio-kinetic model predictions reproduce experimental tendencies. From this base, experimental and stoichio-kinetic models could be progressively complexified to obtain a predictive tool of nutritional quality of meat.

Molecular biological methods are fast and efficient tool for the identification of microorganisms in real samples. The aim of this diploma thesis was analysis of microflora in control and contaminated brined cheeses. DNA isolated from analyzed samples was used to optimize the PCR course using primers with GC clamp on the distribution of amplicons using DGGE. DGGE products were reamplified after optimization and prepared for DNA sequencing. DNA isolated from analyzed samples was used in real-time PCR with high resolution melt analysis of the amplicons (HRMA). Samples of cheese and bacterial cultures isolated from cheeses were compared by DGGE and HRMA. Comparing the position of the amplicons was found that contaminants may be Bacillus licheniformis, Staphylococcus epidermidis, and Acinetobacter baumanii/ calcoaceticus. Sequence analysis of cheese and pickles amplicons, the presence of Bacillus sp. and other microorganisms spree in five genera were detected. Representatives of the tree genera were cultured. It is considered contamination Bacillus sp., or microorganisms which are not culturable methods used. The method is suitable for the analysis of complex microflora in cheese and pickles after further optimization.

Im Rahmen der vorliegenden Arbeit wurde der Einfluss der nichtenzymatischen Glykosylierung auf das Denaturierungsverhalten und die funktionellen Eigenschaften von Molkenproteinen, hier im speziellen die emulgierenden Eigenschaften, untersucht. Nach einer Bestimmung technologisch relevante Glykosylierungsgrade sollten in unterschiedlich glykosylierten Molkenproteinpräparaten das Denaturierungsverhalten sowie die Emulgiereigenschaften in Abhängigkeit vom Glykosylierungsgrad mit unterschiedlichen Methoden bestimmt werden. Der aus praktischer Sicht relevante Einfluss der Glykosylierung auf die sensorischen Eigenschaften wurde einerseits in Molkenproteinlösungen und andererseits in einem komplexen System (Modell-Schmelzkäsezubereitung) erfasst. Schließlich galt es, den Einfluss der Glykosylierung auf die Mikrostruktur und die Festigkeit am Beispiel der Modell- Schmelzkäsezubereitung zu untersuchen und daraus unmittelbare Konsequenzen für die technologische Praxis abzuleiten.

Indiana University-Purdue University Indianapolis (IUPUI) / Anbu is a bacterial protein with significant homology to the sub-units of the 20S proteasome and is predicted to be a novel bacterial proteasome. The goal of this project was to determine if the recombinant Anbu protein from Pseudomonas aeruginosa is a proteasome. Anbu from P. aeruginosa was successfully cloned, expressed and purified. In order to determine the catalytic activity of Anbu, the purified protein was tested with a variety of substrates and conditions. The targets analyzed included fluorescently-labeled substrates, denatured proteins, diubiquitin, and a peptide library in the hopes of obtaining a useful model substrate. Experiments were also conducted to determine what role Anbu has in the cell. Western analysis was performed on the cell lysate of wild type P. aeruginosa and insertional mutants to detect Anbu expression. The level of biofilm formation was compared between the wild type and mutants. Cultures were grown under stress conditions including the oxidative stress of diamide and the nitrosative stress of S-nitrosoglutathione. Growth rates were monitored in an attempt to detect a phenotypic difference between the wild type and the mutants lacking Anbu, HslV, and the other proteins of interest. While a substrate for Anbu has yet to be found, this protein was found to assemble into a larger structure and P. aeruginosa lacking Anbu was sensitive to the oxidative stress of diamide and the nitrosative stress of S-nitrosoglutathione.

Indiana University-Purdue University Indianapolis (IUPUI) / Eukaryotic cells rapidly modulate protein synthesis in response to environmental cues through the reversible phosphorylation of eukaryotic initiation factor 2 (eIF2α~P) by a family of eIF2α kinases. The eIF2 delivers initiator Met-tRNAiMet to the translational apparatus, and eIF2α~P transforms its function from a translation initiation factor into a competitive inhibitor of the guanine nucleotide exchange factor (GEF) eIF2B, which is responsible for the recycling of eIF2-GDP to the translationally-competent eIF2-GTP state. Reduced eIF2-GTP levels lower general protein synthesis, which allows for the conservation of energy and nutrients, and a restructuring of gene expression. Coincident with global translational control, eIF2α~P directs the preferential translation of mRNA encoding ATF4, a transcriptional activator of genes important for stress remediation. The term Integrated Stress Response (ISR) describes this pathway in which multiple stresses converge to phosphorylate eIF2α and enhance synthesis of ATF4 and its downstream effectors. In this study, we used sucrose gradient ultracentrifugation and a genome-wide microarray approach to measure changes in mRNA translation during ER stress. Our analysis suggests that translational efficiencies vary across a broad range during ER stress, with the majority of transcripts being either repressed or resistant to eIF2α~P, while a notable cohort of key regulators are subject to preferential translation. From this latter group, we identify IBTKα as being subject to both translational and transcriptional induction during eIF2α~P in both cell lines and a mouse model of ER stress. Translational regulation of IBTKα mRNA involves the stress-induced relief of two inhibitory uORFs in the 5’-leader of the transcript. Also identified as being subject to preferential translation is mRNA encoding the bifunctional aminoacyl tRNA synthetase EPRS. During eIF2α~P, translational regulation of EPRS is suggested to occur through the bypass of a non-canonical upstream ORF encoded by a CUG start codon, highlighting the diversity by which upstream translation initiation events can regulate expression of a downstream coding sequence. This body of work provides for a better understanding of how translational control during stress is modulated genome-wide and for the processes by which this mode of gene regulation in the ISR contributes to cell fate.

<p dir="ltr">The impacts of processing on protein structure are of broad interest to the food science community including ingredient producers, product developers, and researchers. Processing and isolation steps induce protein structural changes which occur due to temperature based, shear, and chemical inputs, leading to denatured protein with different functionalities. However, exploration of the protein folding landscape as a way to intentionally modify protein conformation is not widely understood in food science. This particularly applies to cold denaturation, which is the structural changes in protein as the result of low temperature treatments.</p><p dir="ltr">This work has two primary goals. The first was to develop understanding of protein conformations resulting from cold denaturation and its implications for food textural properties. Pea protein was selected for this work since it is a source of plant-based protein that has recently grown in popularity and contains many hydrophobic amino acids that would make is susceptible to cold denaturation. Cold denaturation was studied using physicochemical techniques including differential scanning calorimetry, Fourier transform infrared spectroscopy, zeta potential, fluorescence spectroscopy, dynamic light scattering, and rheology. These techniques are used to characterize untreated pea protein, and proteins that have been modified using different combinations of ethanol, shear forces, acidic conditions, extrusion, and temperatures below 0°C. Significant physicochemical differences are found as the result of low temperatures, driven by an increase in surface hydrophobicity and electrostatic interactions. These differences led to protein gelation through hydrophobic forces, changing the nature of gels. Similarly, the increase in protein hydrophobicity leads to more stable emulsions from these products and unique fatty extrudates.</p><p dir="ltr">A second aim of this work developed bioinformatic models to interpret physiochemical data and provide mechanistic understanding of the process, as well as predict functional properties based on protein models. Strong correlations are found for the zeta potential, secondary structure, hydrogen bonds, and surface hydrophobicity. These models are used to convert data into physicochemical energy and used to provide reasonable estimates of mechanical properties of pea protein in extrusion, gelation, and emulsification. Together, this work shows that cold denaturation may be a useful tool for food product developers creating fatty and creamy textures. It also suggests bioinformatic modeling as a tool to estimate protein functionality, which could lead to tremendous time savings in process and product design.</p>

In dieser Arbeit werden systematisch die bisher unerforschten grundlegenden physikalischen und chemischen Eigenschaften von DNA-Origami untersucht, die die Stabilität dieser aus doppelsträngiger DNA aufgebauten nanoskopischen Suprastrukturen bestimmen. In Analogie zu den zahlreichen Studien, die sich mit der Stabilität von Proteinen durch kontrollierte Denaturierung beschäftigen, spielen auch in dieser Arbeit die Denaturierungsbedingungen eine zentrale Rolle. Unter Verwendung von Guanidinium (Gdm+) als teilweise DNA-stabilisierendes, aber auch potentiell denaturierendes Kation steht dessen Wirkung auf DNA-Origami-Dreiecke im Mittelpunkt der Untersuchungen, wobei insbesondere die unerwartete Modulation der nanoskopischen Schädigung von DNA-Origami durch die begleitenden Gegenanionen zu Gdm+ im Vordergrund steht. Die Experimente zielen darauf ab, atomistische, molekulare, nanoskopische und thermodynamische Eigenschaften von DNA-Origami zu korrelieren und zu klären, wie diese vom Design des DNA-Origami selbst abhängen können. Die Ergebnisse zeigen einen unerwarteten Zusammenhang zwischen den spezifischen Gegenanionen des Denaturierungsmittels und der Stabilität der DNA-Origami-Dreiecke: Sulfat wirkt stabilisierend, während Chlorid die Superstruktur bereits unterhalb der globalen Schmelztemperatur destabilisiert. Statistische Analysen von Rasterkraftmikroskop (AFM)-Bildern und Zirkulardichroismus (CD)-Spektren zeigen Strukturübergänge auf nano-skopischer bzw. molekularer Ebene. Werden diese Techniken mit thermischer Denaturierung in Gegenwart von schwacher bis starker chemischer Denaturierung kombiniert, so zeigt sich, dass Änderungen der Wärmekapazität (ΔCp) während der strukturellen Veränderungen der DNA-Originale eine Schlüsselrolle bei der Bestimmung ihrer Empfindlichkeit gegenüber Temperatur und Denaturierungsmitteln spielen. Die Daten deuten darauf hin, dass Wasser auf apolaren DNA-Origami-Oberflächen der molekulare Ursprung der abgeleiteten Wärme-kapazitätsänderungen ist. Diese Hypothese wird durch Molekulardynamik-Simulationen (MD) unterstützt, die die Modulation von ΔCp durch die Hydratationshüllen der Anionen zeigen. Ihr unterschiedliches Potential, stabile Ionenpaare mit Gdm+ in konzentrierten Salzlösungen zu bilden, kann die experimentell beobachteten Variationen der strukturellen Stabilität erklären. Die Kopplung von strukturellen Übergängen an ΔCp wird somit als Schlüsselfaktor für die Destabilisierung von DNA-Origami sowohl bei höheren als auch bei niedrigeren Temperaturen identifiziert. Darüber hinaus weisen DNA-Origami nicht nur diese Eigenschaft auf, sondern ermöglichen auch die Beobachtung von kalten Denaturierungsprozessen auf nanoskopischer Ebene, bei denen kälteinduzierte Spannungen innerhalb der Superstruktur bei einem Bruch an vorherbestimmten lokalen Stellen freigesetzt werden, die in AFM-Bildern sichtbar sind. Dies ist die erste Beobachtung der kälteinduzierten Denaturierung von Nukleinsäuren bei Temperaturen über 0 °C sowie von DNA-basierten Superstrukturen. In dieser Arbeit wird die strukturelle Stabilität von sechs verschiedenen 2D- und 3D-DNA-Origami-Nanostrukturen in unterschiedlichen chemischen Umgebungen untersucht. Drei chaotrope Salze - Guanidiniumsulfat (Gdm2SO4), Guanidiniumchlorid (GdmCl) und Tetrapropylammoniumchlorid (TPACl) - werden als Denaturierungsmittel verwendet. Mittels Rasterkraftmikroskopie wird die Integrität der Nanostrukturen quantifiziert, wobei sich Gdm2SO4 als das schwächste und TPACl als das stärkste Denaturierungsmittel für DNA-Origami erweist, was sich auch in den Schmelztemperaturen widerspiegelt. Die Abhängigkeit der DNA-Origami-Stabilität von der Superstruktur wird besonders bei 3D-Nanostrukturen deutlich. Hier zeigen mechanisch flexible Designs sowohl in GdmCl als auch in TPACl eine höhere Stabilität als ihre starren Gegenstücke. Die Abhängigkeit der DNA-Origami-Stabilität von der Superstruktur wird besonders in 3D-Nanostrukturen deutlich, in denen mechanisch flexible Strukturen sowohl in GdmCl als auch in TPACl eine höhere Stabilität aufweisen als ihre steifen Gegenstücke. Dies begünstigt die Bildung von intramolekularen Verformungen, die sich entweder in 'weichen' Architekturen über die gesamte Superstruktur verteilen oder in ansonsten 'steifen' Strukturen in den weniger stabilen Regionen konzentrieren.:Table of contents Questions addressed in this thesis .................................................................................... I Abstract ................................................................................................................................ I Englisch .................................................................................................................................................. I Deutsch .................................................................................................................................................. II Acronyms ........................................................................................................................... III Substances .......................................................................................................................................... IV Physical and Chemical abbreviations ............................................................................................... IV Mathematical abbreviations ................................................................................................................ V 1 Introduction ................................................................................................................. 1 1.1 Deoxyribonucleic acid ................................................................................................................. 1 1.1.1 The structure of DNA ............................................................................................................ 1 1.1.2 Hydrogen bonds .................................................................................................................... 1 1.1.3 Base stacking ........................................................................................................................ 2 1.1.4 Water DNA interactions: A complex dance of stability and dynamics .................................. 5 1.1.5 The effect of ionic strength on DNA conformation ................................................................ 9 1.1.6 Conformational changes ....................................................................................................... 9 1.1.7 Forms of DNA ..................................................................................................................... 10 1.1.8 The role of apolar groups in DNA unfolding ........................................................................ 13 1.1.9 Energetics of DNA structural transitions ............................................................................. 14 1.1.10 Melting temperature ............................................................................................................ 15 1.2 Hofmeister series ....................................................................................................................... 17 1.2.1 Probing the Hofmeister series: Salt effects biomolecules ................................................... 17 1.2.2 Specific ion effects in electrolyte solutions .......................................................................... 19 1.3 DNA nanostructures................................................................................................................... 20 1.3.1 DNA origami ........................................................................................................................ 22 1.3.2 Challenges in DNA origami stability .................................................................................... 26 1.3.3 DNA origami in single molecule studies .............................................................................. 27 1.4 Circular dichroism ...................................................................................................................... 28 1.4.1 Circular dichroism spectroscopy for analyzing DNA conformations ................................... 30 1.4.2 Wavelength-dependent spectroscopic signatures of DNA conformation ........................... 32 1.5 Atomic force microscopy .......................................................................................................... 34 1.6 2D correlation spectroscopy ..................................................................................................... 36 1.6.1 2D correlation spectroscopy: Synchronous and asynchronous spectra analysis ............... 39 1.6.2 Perturbation-correlation moving-window 2D correlation spectroscopy ............................... 40 1.7 Multivariate analysis of spectral data using PCA and ITTFA ................................................ 41 1.8 Cold denaturation ....................................................................................................................... 42 2 Results and Discussion ............................................................................................ 44 2.1 Cold denaturation of the Rothemund DNA origami triangle .................................................. 45 2.2 Heat denaturation of the Rothemund DNA origami triangle .................................................. 50 2.2.1 Investigations by atomic force microscopy ......................................................................... 51 2.2.2 Circular dichroism spectroscopy and thermodynamic modelling ........................................ 56 2.2.3 Divergent effects of Cl- and SO42- on DNA origami stability ................................................ 62 2.3 Magnesium concentration modulation of DNA Origami heat denaturation ......................... 65 2.4 Assessing DNA origami stability in different chaotropic environments .............................. 66 2.4.1 DNA origami integrity influenced by Gdm2SO4 ................................................................... 67 2.4.2 DNA origami integrity influenced by GdmCl ........................................................................ 73 2.4.3 DNA origami integrity influenced by TPACl ........................................................................ 75 2.4.4 Quantitative comparison ..................................................................................................... 77 3 Critics ......................................................................................................................... 78 4 Conclusion ................................................................................................................. 79 5 Outlook ...................................................................................................................... 81 6 Material and Methods ................................................................................................ 82 6.1 DNA origami synthesis .............................................................................................................. 82 6.2 Sample preparation and AFM imaging ..................................................................................... 82 6.2.1 Anion-specific structure and stability of guanidinium-bound DNA origami & Cold denaturation of DNA origami nanostructures ...................................................................... 82 6.2.2 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 83 6.2.3 Cold denaturation of DNA origami nanostructures ............................................................. 83 6.3 CD spectroscopy and analysis ................................................................................................. 84 6.3.1 Anion-specific structure and stability of guanidinium-bound DNA origami ......................... 84 6.3.2 Pre-treatment of the CD data and calculation of melting temperatures .............................. 84 6.3.3 Cold denaturation of DNA origami nanostructures ............................................................. 84 6.3.4 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 84 6.4 Principal component analysis and iterative target test factor analysis ............................... 85 6.5 Thermodynamic modelling ........................................................................................................ 85 6.6 Molecular dynamics modelling ................................................................................................. 85 Appendix ........................................................................................................................... 88 Acknowledgment ............................................................................................................ 100 Bibliography .................................................................................................................... 101 List of Figures ................................................................................................................. 116 List of Tables ................................................................................................................... 118 Declaration of independence – Selbstständigkeitserklärung ...................................... 119 / This thesis undertakes the systematic study of hitherto unexplored fundamental physical and chemical properties of DNA origami that determine the stability of these designed nanoscopic superstructural assemblies of double-stranded DNA. In analogy to the vast number of studies addressing protein stability by controlled denaturation, denaturing conditions play a central role in this thesis as well. Using guanidinium (Gdm+) as a partly DNA-stabilizing but also potentially denaturing cation, its effect on DNA origami triangles is central to the study which particularly addressed the unexpected modulation of nanoscopic damage of DNA origami by the accompanying counter-anions to Gdm+. The experiments aim at correlating atomistic, molecular, nanoscopic and thermodynamic properties of DNA origami and at elucidating how these may depend on the DNA origami design itself. The results demonstrate an unexpected relationship between the specific counter-anions of the denaturant and the stability of DNA origami triangles: sulphate exhibits stabilizing effects and chloride induces destabilization of the superstructure already below the global melting temperature. Statistical analyses of both atomic force microscopy (AFM) images and circular dichroism (CD) spectra reveal structural transitions at the nanoscopic and molecular level, respectively. Combining these techniques with thermal denaturation in the presence of mild to strong chemical denaturation, changes in heat capacity (ΔCp) during DNA origami structural changes are shown to play the key role in determining their sensitivity to temperature and denaturants. The data suggest that water at apolar DNA origami surfaces is the molecular origin of the derived heat capacity changes. This hypothesis is substantiated by Molecular Dynamics (MD) simulations which shed light on the modulation of ΔCp by the hydration shells of anions. Their different potential to form stable ion pairs with Gdm+ in concentrated salt solutions can explain the experimentally observed variations of structural stability. The coupling of structural transitions to ΔCp is thus identified as a key factor in the destabilization of DNA origami at both elevated and lowered temperatures. Furthermore, DNA origami not only exhibit this property, but also enable the observation of cold denaturation processes at the nanoscopic level, where cold-induced strain within the superstructure is released upon breakage at predisposed local sites, visible in AFM images. This is the first observation of cold-induced denaturation of nucleic acids at temperatures above 0 °C, as well of DNA-based superstructures. Extending the scope, the work evaluates the structural stability of six different 2D and 3D DNA origami nanostructures in different chemical environments. Three chaotropic salts - guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl) - are used as denaturants. Atomic force microscopy quantifies the nanostructural integrity, revealing Gdm2SO4 as the weakest and TPACl as the strongest DNA origami denaturant, which is also reflected in the melting temperatures. The dependence of DNA origami stability on its superstructure is particularly evident in 3D nanostructures, where mechanically flexible designs exhibit higher stability in both GdmCl and TPACl than rigid counterparts. This supports the buildup of intramolecular strain, which becomes either partitioned among the entire superstructure in “soft” architectures or accumulates at the least stable regions in otherwise “rigid” designs.:Table of contents Questions addressed in this thesis .................................................................................... I Abstract ................................................................................................................................ I Englisch .................................................................................................................................................. I Deutsch .................................................................................................................................................. II Acronyms ........................................................................................................................... III Substances .......................................................................................................................................... IV Physical and Chemical abbreviations ............................................................................................... IV Mathematical abbreviations ................................................................................................................ V 1 Introduction ................................................................................................................. 1 1.1 Deoxyribonucleic acid ................................................................................................................. 1 1.1.1 The structure of DNA ............................................................................................................ 1 1.1.2 Hydrogen bonds .................................................................................................................... 1 1.1.3 Base stacking ........................................................................................................................ 2 1.1.4 Water DNA interactions: A complex dance of stability and dynamics .................................. 5 1.1.5 The effect of ionic strength on DNA conformation ................................................................ 9 1.1.6 Conformational changes ....................................................................................................... 9 1.1.7 Forms of DNA ..................................................................................................................... 10 1.1.8 The role of apolar groups in DNA unfolding ........................................................................ 13 1.1.9 Energetics of DNA structural transitions ............................................................................. 14 1.1.10 Melting temperature ............................................................................................................ 15 1.2 Hofmeister series ....................................................................................................................... 17 1.2.1 Probing the Hofmeister series: Salt effects biomolecules ................................................... 17 1.2.2 Specific ion effects in electrolyte solutions .......................................................................... 19 1.3 DNA nanostructures................................................................................................................... 20 1.3.1 DNA origami ........................................................................................................................ 22 1.3.2 Challenges in DNA origami stability .................................................................................... 26 1.3.3 DNA origami in single molecule studies .............................................................................. 27 1.4 Circular dichroism ...................................................................................................................... 28 1.4.1 Circular dichroism spectroscopy for analyzing DNA conformations ................................... 30 1.4.2 Wavelength-dependent spectroscopic signatures of DNA conformation ........................... 32 1.5 Atomic force microscopy .......................................................................................................... 34 1.6 2D correlation spectroscopy ..................................................................................................... 36 1.6.1 2D correlation spectroscopy: Synchronous and asynchronous spectra analysis ............... 39 1.6.2 Perturbation-correlation moving-window 2D correlation spectroscopy ............................... 40 1.7 Multivariate analysis of spectral data using PCA and ITTFA ................................................ 41 1.8 Cold denaturation ....................................................................................................................... 42 2 Results and Discussion ............................................................................................ 44 2.1 Cold denaturation of the Rothemund DNA origami triangle .................................................. 45 2.2 Heat denaturation of the Rothemund DNA origami triangle .................................................. 50 2.2.1 Investigations by atomic force microscopy ......................................................................... 51 2.2.2 Circular dichroism spectroscopy and thermodynamic modelling ........................................ 56 2.2.3 Divergent effects of Cl- and SO42- on DNA origami stability ................................................ 62 2.3 Magnesium concentration modulation of DNA Origami heat denaturation ......................... 65 2.4 Assessing DNA origami stability in different chaotropic environments .............................. 66 2.4.1 DNA origami integrity influenced by Gdm2SO4 ................................................................... 67 2.4.2 DNA origami integrity influenced by GdmCl ........................................................................ 73 2.4.3 DNA origami integrity influenced by TPACl ........................................................................ 75 2.4.4 Quantitative comparison ..................................................................................................... 77 3 Critics ......................................................................................................................... 78 4 Conclusion ................................................................................................................. 79 5 Outlook ...................................................................................................................... 81 6 Material and Methods ................................................................................................ 82 6.1 DNA origami synthesis .............................................................................................................. 82 6.2 Sample preparation and AFM imaging ..................................................................................... 82 6.2.1 Anion-specific structure and stability of guanidinium-bound DNA origami & Cold denaturation of DNA origami nanostructures ...................................................................... 82 6.2.2 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 83 6.2.3 Cold denaturation of DNA origami nanostructures ............................................................. 83 6.3 CD spectroscopy and analysis ................................................................................................. 84 6.3.1 Anion-specific structure and stability of guanidinium-bound DNA origami ......................... 84 6.3.2 Pre-treatment of the CD data and calculation of melting temperatures .............................. 84 6.3.3 Cold denaturation of DNA origami nanostructures ............................................................. 84 6.3.4 Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants ........................................................................................................ 84 6.4 Principal component analysis and iterative target test factor analysis ............................... 85 6.5 Thermodynamic modelling ........................................................................................................ 85 6.6 Molecular dynamics modelling ................................................................................................. 85 Appendix ........................................................................................................................... 88 Acknowledgment ............................................................................................................ 100 Bibliography .................................................................................................................... 101 List of Figures ................................................................................................................. 116 List of Tables ................................................................................................................... 118 Declaration of independence – Selbstständigkeitserklärung ...................................... 119

Tesis por compendio / [ES] El desarrollo científico y tecnológico de las últimas décadas ha dado lugar a sistemas sensores capaces de obtener, procesar y transmitir información sobre multitud de aspectos físicos y químicos, y utilizarla para mejorar aspectos clave de multitud de áreas de nuestra sociedad. Los sensores químicos son dispositivos compactos y miniaturizados capaces de ofrecer soluciones alternativas a las técnicas de análisis instrumental convencionales. En especial, los biosensores han adquirido gran relevancia por los avances que han supuesto para sectores estratégicos como el diagnóstico clínico, la industria alimentaria y el medio ambiente. Los biosensores ópticos se basan en interacciones entre la luz y la materia para transducir eventos de bioreconocimiento y presentan prestaciones importantes como la estabilidad, inmunidad a estímulos externos y versatilidad en el desarrollo de aproximaciones sin marcaje (label-free). Este último aspecto suele aprovechar fenómenos nanoscópicos y su desarrollo se encuentra muy ligado al progreso de la nanociencia y nanotecnología. Un aspecto clave en el biosensado sin marcaje consiste en descubrir y desarrollar nuevas estrategias de transducción. En este sentido, aunque se encuentren aun en una etapa temprana de desarrollo, los biosensores difractivos presentan un gran potencial en términos de simplicidad, miniaturización, y capacidad para minimizar señales no deseadas fruto de interacciones no específicas, entre otros aspectos. / [CA] El desenvolupament científic i tecnològic de les últimes dècades ha donat lloc a sistemes sensors capaços d'obtindre, processar i transmetre informació sobre multitud d'aspectes físics i químics, i utilizar-la per a millorar aspectes clau de multitud d'arees de la nostra societat. Els sensors químics són dispositius compactes i miniaturitzats capaços d'oferir solucions alternatives a les tècniques d'analisi instrumental convencionals. Especialment, els biosensors han adquirit gran rellevància pels avanços que han suposat per als sectors estratègics com el diagnòstic clínic, la industria alimentària i el medi ambient. Els biosensors òptics es basen en interaccions entre la llum i la matèria per a transduir esdeveniments de bioreconèixement i presenten prestacions importants com estabilitat, immunitat a estímuls externs i versatilitat en el desenvolupament d'aproximacions sense marcatge (label-free). Aquest últim aspecte sol aprofitat fenòmens nanoscòpics i el seu desenvolupament es troba molt lligat al progrés de la nanociència i nanotecnologia. Un aspecte clau en el biosensat sense marcatge consisteix a descobrir i desenvolupar noves estratègies de transducció. En aquest sentit, encara que es troben fins i tot en una etapa primerenca de desenvolupament, els biosensors difractius presenten un gran potencial en termes de simplicitat, miniaturització, i capacitat per a minimitzar senyals no desitjats fruit d'interaccions no específiques, entre altres aspectes. / [EN] The scientific and technological progress in recent decades has given rise to sensor systems capable of obtaining, processing, and transmitting information on a multitude of physical and chemical aspects and using it to improve key aspects of many areas of our society. Chemical sensors are compact, miniaturized devices capable of offering alternative solutions to conventional instrumental analysis techniques. In particular, biosensors have become highly relevant due to the progress they have brought to strategic sectors such as clinical diagnostics, the food industry, and the environment. Optical biosensors rely on interactions between light and matter to transduce biosensing events and provide important features such as stability, immunity to external stimuli, and versatility in the development of label-free approaches. This last aspect usually exploits nanoscopic phenomena and its development in closely linked to the progress in nanoscience and nanotechnology. A key aspect of label-free biosensing is the discovery and development of new transduction strategies. In this regard, although they are at an early stage of development, diffractive biosensors offer great potential in terms of simplicity, miniaturization, and the ability to minimize unwanted signals from non-specific interactions, among other aspects. / This work was financially supported by the Ministerio de Ciencia e Innovación/Agencia Estatal de Investigación (MCIN/AEI/10.13039/501100011033) co-funded by the European Union “ERDF A way of making Europe” (PID2019-110713RB-I00, TED2021-132584B-C21, PID2019-110877GB-I00), Ministerio de Economía y Competitividad (TEC2016-80385-P), Generalitat Valenciana (PROMETEO/2019/048 PROMETEO/2020/094, PROMETEO/2021/015, IDIFEDER/2021/046). A.J.D. ackowledges the FPI-UPV 2017 grant program. The authors acknowledge Instituto de Microelectrónica de Barcelona CNM-CSIC for the support in the fabrication of the measured chip samples on the Multiproject CNM-VLC silicon nitride technology platform. / Juste Dolz, AM. (2023). Biogratings: Diffractive Transducers for Biosensing in Photonic Platforms [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/194251 / Compendio