-------------------------------Abstract--------------------------------Since the prediction by Maria Göppert-Mayer in the thirties of the possibility for a fluorescent molecule to be simultaneously excited by multiple photons and, more recently, the development of pulsed lasers, multiphoton microscopy has gradually evolved to finally become one of the most used fluorescent imaging techniques for the studies of thick scattering tissues or for in vivo observations of animals. Either for neurological, physiological or morphological studies, the non invasiveness and the limitation of the excited volume to the focal volume have made this fluorescence microscopy technique an essential tool for biologists.However, in a world where the biological studies always require better microscopes and where there is always a need for the spatial resolution to be improved, it is essential to offer techniques allowing to obtain a better resolution in the three dimensions and to access resolution beyond the diffraction limit defined by Ernst Abbe more than a century ago. In this thesis, the saturated excitation of fluorescence technique is adapted to multiphoton microscopy. This method achieves super-resolved images by temporally modulating the excitation laser-intensity and by demodulating the higher harmonics from the saturated fluorescence signal. As a proof of principle, the improvement of the lateral and axial resolution has been measured on a sample of fluorescent microspheres. While the third harmonic already provides an enhanced resolution, we show in this work that a further improvement can be obtained with an appropriate linear combination of the demodulated harmonics.In the end, a near twofold improvement of the resolution has been obtained in the lateral but also in the axial directions. This improvement is in agreement with the estimated resolution improvement predicted in the theoretical and the mathematical analysis of the technique carried out in this work.We also present in vitro imaging of fluorescent microspheres incorporated in HeLa cells. Enhancements of lateral and axial resolution has been observed, showing that this super-resolution technique performs well in biological samples.Finally, the strengths and weaknesses of the technique have also been analysed and detailed to see in which niche in the world of biological imaging this method can find its place. To this end, its characteristics are compared to other super-resolution and super-localisation techniques that have been previously studied in this thesis.It points out that the imaging depth, the non invasiveness and the relatively low illumination power on the samples but also the limitation of the excited volume in multiphoton microscope coupled with the simple and cost-effective implementation as well as the relatively low illumination power on the sample used in the saturated excitation technique make this method an excellent candidate for deep in vivo studies trough scattering tissue like the skin. / -----------------------Résumé-----------------------Depuis la prédiction de Maria Göppert-Mayer dans les années 30 de la possibilité pour une molécule fluorescente d'être excitée simultanément par plusieurs photons et, plus récemment, depuis le développement des lasers pulsés, la microscopie multiphotonique s'est peu à peu développée pour finalement s'imposer aujourd'hui comme un des outils d'observation par fluorescence les plus performants pour les études de tissus épais diffusants, ou encore pour l'observation in vivo d'animaux. Que ce soit pour des études neurologiques, physiologiques ou morphologiques, l'aspect non invasif et la limitation du volume excité au volume focal ont rendu cet outil de microscopie indispensable aux biologistes.Cependant, dans un monde où les études biologiques nécessitent toujours de meilleurs microscopes et où la résolution spatiale en particulier doit toujours être améliorée, il convient de proposer des techniques permettant d'obtenir une meilleure résolution dans les trois dimensions et d'aller au-delà de la limite de diffraction définie par Ernst Abbe il y a plus d'un siècle.Dans cette thèse, la technique de saturation de l'excitation de la fluorescence est adaptée à la microscopie multiphotonique. Cette méthode permet d'obtenir des images de superrésolution en modulant temporellement l'intensité laser d'excitation et en démodulant les harmoniques supérieures présentes dans le signal saturé de fluorescence. La démonstration de principe sur des microsphères fluorescentes a été réalisée montrant une amélioration de la résolution latérale et axiale. Alors que l'utilisation de la troisième harmonique produit déjà une meilleure résolution, ce travail de thèse montre qu'une amélioration supplémentaire peut être obtenue en utilisant une combinaison linéaire particulière des harmoniques démodulées.Au final, un quasi doublement de la résolution a pu être observé tant dans les directions latérales que dans la direction axiale. Cette amélioration correspond à l'amélioration prédite dans l'analyse théorique et mathématique réalisée également dans ce travail.De plus, le passage aux études in vitro a été réalisé avec succès en observant des microsphères fluorescentes incorporées dans des cellules HeLa. Des améliorations de la résolution latérale et axiale ont également été observées montrant que cette technique de superrésolution peut être appliquée à l'étude d'échantillons biologiques. Les forces et les faiblesses de cette méthode sont également analysées et détaillées afin de voir dans quel créneau d'études biologiques la technique de saturation de l'excitation de fluorescence pourrait se faire une place. A cette fin, ses caractéristiques sont comparées aux autres méthodes de superrésolution et de superlocalisation détaillées dans la première partie de ce travail.Il en resort que l'importante profondeur d'imagerie, l'aspect non invasif et la limitation du volume excité de la microscopie multiphotonique couplés à la simplicité d'implémentation et les relativement faibles puissances utilisées pour saturer l'excitation font de cette technique un excellent candidat pour des études in vivo dans des zones en profondeur dans des milieux diffusants comme la peau. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

Microscopy techniques have been developed and refined over multiple decades, but innovation around single photon modalities has slowed. The advancement of the utility of information acquired, and minimum resolution available is seemingly reaching an asymptote. The fusion of light microscopy and well-studied nonlinear processes has broken through this barrier and enabled the collection of vast amounts of additional information beyond the topographical information relayed by traditional microscopes. Through nonlinear imaging modalities, chemical information can also be extracted from tissue. Nonlinear microscopy also can beat the resolution limit caused by diffraction, and offers up three-dimensional capabilities. The power of nonlinear imaging has been demonstrated by countless research groups, solidifying it as a major player in biomedical imaging. The value of a nonlinear imaging system could be enhanced if a reduction in size would permit the insertion into bodily cavities, as has been demonstrated by linear imaging endoscopes. The miniaturization of single photon imaging devices has led to significant advancements in diagnostics and treatment in the medical field. Much more information can be extracted from a patient if the tissue can be imaged in vivo, a capability that traditional, bulky, table top microscopes cannot offer. The development of new technologies in optics has enabled the miniaturization of many critical components of standard microscopes. It is possible to combine nonlinear techniques with these miniaturized elements into a portable, hand held microscope that can be applied to various facets of the biomedical field. The research demonstrated in this thesis is based on the selection, testing and assembly of several miniaturized optical components for use as a nonlinear imaging device. This thesis is the first demonstration of a fibre delivered, microelectromechanical systems mirror with miniaturized optics housed in a portable, hand held package. Specifically, it is designed for coherent anti-Stokes Raman scattering, second harmonic generation, and two-photon excitation fluorescence imaging. Depending on the modality being exploited, different chemical information can be extracted from the sample being imaged. This miniaturized microscope can be applied to diagnostics and treatments of spinal cord diseases and injuries, atherosclerosis research, cancer tumour identification and a plethora of other biomedical applications. The device that will be revealed in the upcoming text is validated by demonstrating all designed-for nonlinear modalities, and later will be used to perform serialized imaging of myelin of a single specimen over time.

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Master of Science / Department of Physics / Brett D. Esry / The two-state field-aligned (1-D) model has been employed to investigate the dissociation dynamics of a hydrogen molecular ion and its isotopes under the Born-Oppenheimer approximation without rotation. The emphasis of this work was on the role of mass during the dynamical dissociation processes and on the laser-induced branching ratios between different photon pathways. Firstly, we have found that scaling the pulse duration of the laser pulse, applied to H[subscript]2+ and D[subscript]2+ , by the square root of the mass ratio of these isotopes will produce similar structure in the nuclear kinetic energy release (KER) spectra. In fact, the similarity of the spectra is enhanced by including some averaging that is necessary for comparison with experiment. For this to occur, the same broad initial vibrational distribution and a short pulse are preferred. Using this scaling idea, it is possible to produce effectively shorter laser pulses by studying heavier isotopes, like D[subscript]2+. Secondly, we have demonstrated analytically and numerically that there is a carrier-envelope phase effect in the total dissociation probability (TDP) of H[subscript]2+, and this effect grows with nuclear mass. We further show that under the same laser conditions, the CEP effect in the asymmetry between breakup channels decreases with mass. Our analytic expressions enhance the idea that CEP effects can be understood as an interference between different n-photon processes. Thirdly, the trends in the dissociation dynamics of H[subscript]2+ and D[subscript]2+ in a 800nm ultra short intense laser field were demonstrated by studying the dissociation branching ratios of multiphoton processes as a function of the laser peak intensity (from 8[times]10[superscript]9 to 10[superscript]14 W/cm[superscript]2) or pulse length (5fs-7.5fs). Based on the two-state approximation, an energy-analysis method (EAM) was employed to separate multiphoton processes. The results show that the one-photon dissociation process dominates over all other photon processes under all the laser conditions applied in the calculations and that the zero-photon process contributes to a surprisingly large fraction of the total dissociation. Two- and three- photon dissociation are weaker processes, but become more and more important as the laser peak intensity and pulse length increases. A two-state Floquet method was used to check the accuracy of the EAM, and good agreement between the two methods was found, demonstrating the reliability of the EAM. In comparison with H[subscript]2+, D[subscript]2+ displays stronger two and three photon branching ratios (above-threshold dissociation - ATD), which can be attributed to the late arrival of D[subscript]2+ to the critical distance for ATD to occur due to its heavier mass. Therefore, this "mass" effect can be used to steer the molecular dissociation pathways.

Broadband spectral content is required to support ultrashort pulses. However this broadband content is subject to dispersion and hence the pulse duration of corresponding ultrashort pulses may be stretched accordingly. I used a commercially-available adaptive ultrashort pulse shaper featuring multiphoton intrapulse interference phase scan technology to characterise and compensate for the dispersion of the optical system in situ and conducted experimental and theoretical studies in various inter-linked topics relating to the light-matter interaction. Firstly, I examined the role of broadband ultrashort pulses in novel light-matter interacting systems involving optically co-trapped particle systems in which inter-particle light scattering occurs between optically-bound particles. Secondly, I delivered dispersion-compensated broadband ultrashort pulses in a dispersive microscope system to investigate the role of pulse duration in a biological light-matter interaction involving laser-induced cell membrane permeabilisation through linear and nonlinear optical absorption. Finally, I examined some of the propagation characteristics of broadband ultrashort pulse propagation using a computer-controlled spatial light modulator. The propagation characteristics of ultrashort pulses is of paramount importance for defining the light-matter interaction in systems. The ability to control ultrashort pulse propagation by using adaptive dispersion compensation enables chirp-free ultrashort pulses to be used in experiments requiring the shortest possible pulses for a specified spectral bandwidth. Ultrashort pulsed beams may be configured to provide high peak intensities over long propagation lengths, for example, using novel beam shapes such as Bessel-type beams, which has applications in biological light-matter interactions including phototransfection based on laser-induced cell membrane permeabilisation. The need for precise positioning of the beam focus on the cell membrane becomes less strenuous by virtue of the spatial properties of the Bessel beam. Dispersion compensation can be used to control the temporal properties of ultrashort pulses thus permitting, for example, a high peak intensity to be maintained along the length of a Bessel beam, thereby reducing the pulse energy required to permeabilise the cell membrane and potentially reduce damage therein.

Selective gas-phase dissociation strategies have been developed for the characterization of cross-linked peptides and proteins in quadrupole ion trap mass spectrometers. An infrared chromogenic cross-linker (IRCX) containing a phosphotriester afforded rapid differentiation of cross-linked peptides from unmodified ones in proteolytic digests of cross-linked proteins by selective infrared multiphoton dissociation (IRMPD). Only the cross-linked peptides containing the chromogenic phosphate underwent IRMPD and unmodified peptides were not affected by IR irradiation. IRMPD of IRCX-cross-linked peptides yielded uncross-linked y-ion sequence tags of the constituent peptides due to secondary dissociation of all primary product ions which contained the chromophore, thus allowing successful de novo sequencing of the cross-linked peptides. Peptides cross-linked via a two-step conjugation strategy through the formation of a bis-arylhydrazone (BAH) bond were selectively dissociated by ultraviolet radiation at 355 nm. The BAH-cross-linked peptides could be distinguished from not only unmodified peptides but also dead-end modified peptides based on the selectivity of ultraviolet photodissociation. In a complementary approach, electron transfer dissociation of BAH-cross-linked peptides resulted in preferential cleavage of the hydrazone bond which produced two modified peptides. These modified peptides were subsequently interrogated by CID which allowed for the original site of cross-linking to be pinpointed. IRMPD was implemented in a dual pressure linear ion trap to demonstrate successful photodissociation of peptides having modest absorptivities. Peptides were observed to efficiently dissociation by IR irradiation exclusively in the low pressure cell whereas no dissociation was observed in the high pressure cell due to extensive collisional cooling. IRMPD provided greater sequence coverage of the peptides than CID and yielded product ion mass spectra which were predominantly composed of singly charged product ions which simplified spectral interpretation. IRMPD was further applied for the sequencing of small-interfering RNA. Complete sequence coverage was obtained and the results were compared to CID. / text

L’avènement des lasers impulsionnels nanosecondes à femtosecondes a permis un développement rapide de techniques permettant de sonder et/ou de transformer les matériaux à l’échelle locale par des processus d’absorption non linéaire. Ce saut technologique a vu l’émergence de nombreuses applications associées au phénomène de confinement spatial. La stéréolithographie 3D par photopolymérisation biphotonique constitue un exemple typique d’application à forte valeur ajoutée qui offre de prometteuses perspectives en terme d’écriture à l’échelle nanométrique. Un enjeu fondamental constitue alors l’élaboration de nouveaux photoamorceurs très réactifs et activables à deux photons. Dans ce contexte, ce manuscrit présente une étude photophysique et photochimique de deux séries de photoamorceurs biphotoniques ‘Donneur/Accepteur’ intégrants des stilbènes comme relais électroniques avec pré-organisation dans des structures bichromophores. Les processus primaires photoinduits, les mécanismes de photoamorçage, la photoréactivité à l’echelle locale sont décrits et étudiés méthodiquement. Enfin, le potentiel appliqué de cette nouvelle génération de photoamorceurs est mis en évidence en microfabrication multiphotonique à travers l’élaboration de structure 3D à l’échelle µm. / The advent of pulsed laser technologies has promoted the rapid growth of new emerging research domains which aim at probing and/or transforming materials at local scale using non linear absorption processes. A large range of applications takes benefit of the inherent spatial containment observed in non linear absorption processes so as to control photoreactions at nm-scale. The field of multiphoton fabrication (or stereolithography) addresses this fundamental issue and has developed rapidly so that it is no longer a rapid prototyping technology but a real manufacturing technique that is commercially available. The development of multiphoton stereolitography also requires highly reactive two-photon activable (2PA) initiators whose design and elaboration are the subject of considerable molecular engineering research. In this context, the present manuscript describes the photophysical and photochemical properties of two series of 2PA initiators. Such novel D--A structures have be designed by associating distinctive Donor and Acceptor groups into stilbene arms used as ‘electron relay’ and organized into a (multi)branched architecture. The photoinduced primary processes, the global photoinitiating mechanisms as well as the photoreactivity are described methodically. We finally demonstrate the applied potential of this new type of two-photon initiators in multiphoton stereolitography.

Plusieurs facteurs conduisent à la génération de radicaux libres oxydants dans les organismes qui endommagent les biomolécules et en particulier les protéines du vivant. L’une des cibles de l’oxydation dans les protéines est la méthionine (Met). Son oxydation provoque des effets très dommageables, comme la maladie d’Alzheimer ou les maladies à prion. Nous avons étudié la réaction des radicaux hydroxyle (•OH) et de l’état triplet de la 3-carboxybenzophénone (3CB*) avec ces peptides. Le but de ce travail était de caractériser les espèces transitoires et les produits stables formés après oxydation radiolytique et photolytique de peptides contenant la Met (les dipeptides contenant de la Met et les pepetides plus longs tels que la bradykinine, une hormone humaine importante impliquée dans la diminution de la pression artérielle). Nous avons utilisé la photolyse éclair laser (LFP) et la radiolyse pulsée (PR) (pour les espèces transitoires de courte durée de vie), tandis que la radiolyse gamma et la photolyse continue (pour obtenir une caractérisation des produits stables). Les modifications structurelles ont été caractérisées par des techniques de HPLC et par couplage de la spectrométrie de masse (MS) et la détection par spectrométrie infrarouge couplée à la MS (IRMPD, CLIO laser à électrons libres). En outre, il nous a paru intéressant d’étudier deux autres dérivés de la benzophénone (BP), l’oxybenzone (OXB) et le sulisobenzone (SB), qui sont largement utilisés dans les produits de protection solaire commerciaux. En effet, l’application d’écrans solaires est controversée car certaines études épidémiologiques ont indiqué un risque accru de mélanome malin pour leurs utilisateurs. L’oxydation de dipeptides contenant Met par les radicaux •OH ou photosensibilisée par la ³(CB)* a conduit à la formation de radicaux cations centrés sur le soufre de la Met (>S•⁺) qui ont été en outre stabilisés par la formation de liaison deux centres à trois électrons (S∴Y)⁺, Y étant un atome possédant un doublet libre, ou qui ont subi une déprotonation donnant les radicaux contrés sur le carbone en α (α-S). L’oxydation des dipeptides par •OH a abouti à la formation de sulfoxyde de Met (MetSO) en tant que produit principal. Sans aucun doute, l’identification et la caractérisation des MetSO en solutions désoxygénées contenant la catalase est une étape importante dans la quête de produits stables. Toutefois, dans certains cas, d’autres produits ont été identifiés. En ce qui concerne, les produits stables de photolyse, ce sont des adduits avec le groupement 3CB, probablement résultant de la réaction de recombinaison radical-radical. Un autre produit formé au cours de la photolyse était 3CB-3CB résultant d’une photo-addition, qui a une structure similaire à celle du produit d’irradiations de la BP. Tous les produits identifiés (MetSO et la photo-adduits) ont été formés à partir des radicaux α-S par l’intermédiaire d’une dismutation ou une réaction avec 3CBH•/3CB•⁻. L’oxydation de la Met-Lys-bradykinine (MKBR) a abouti à la formation de photo-adduits similaires par réaction sensibilisée avec 3CB. L’oxydation induite de MKBR par •OH a abouti à plusieurs produits, en accord avec la non sélectivité des radicaux •OH. L’un des principaux produits est le MetSO et la phénylalanine hydroxylée. Notons que l’arginine n’est pas oxydée. Enfin, la photolyse de SB et OXB a été étudiée à l’aide de photolyse éclair au laser femto-et nanoseconde, ainsi que l’oxydation à un électron de ces molécules par radicaux •OH ont été réalisées en PR. Les résultats obtenus ont été comparés à ceux d’autres dérivés de la BP. L’état singulet excité subit un quenching à 100 % par transfert de proton intraomléculaire à l’état excité (ESIPT) en milieu aprotique et en milieu non polaire. Dans le cas d’un solvant polaire, la formation de radicaux phénoxyles a été identifiée. La réactivité des filtres solaires UV-excité vers dérivés simples de méthionine est également en cours d’étude. / Several factors (radiation, metabolism, pollutants) lead to the generation of oxidizing free radicals in living organisms that damage all biomolecules and especially proteins. One of the protein targets is Methionine (Met). Its oxidation causes highly damaging effects, such as Alzheimer’s or prion disease. The aim of this work was to investigate the transient species and the stable products formed after radiolytic and photolytic oxidation of Met-containing peptides. The reaction of hydroxyl radicals (•OH) and 3-carboxybenzophenone triplet state with Met-residue in peptides was investigated for model compounds (Met-dipeptides) and for longer peptides (e.g. Bradykinin). Laser flash photolysis and pulse radiolysis were used to characterize short-lived transient species, while gamma radiolysis and steady-state photolysis were used for quantitative and qualitative characterization of stable products. The structural modifications induced by oxidation have been characterized by the HPLC coupled with mass spectrometry and Infrared Multi Photon Dissociation Spectroscopy (IRMPD, CLIO Free electron laser). The oxidation of investigated Met-containing compounds by •OH or 3CB* led to the formation of S-centered radical cation >S•+ on Met-residue, that were further stabilized by formation of two-centered three-electron bond (S∴Y)+ or underwent the deprotonation reaction yielding the α-(alkylthio)alkyl radicals (α-S). The oxidation of Met-containing dipeptides by •OH radicals yielded the formation of Met sulfoxide (MetSO) as a main product. Undoubtedly, the identification and characterization of MetSO in deoxygenated solutions containing catalase was a milestone in investigation of stable products. However, in some cases, other products were identified. The stable products of photolysis were adducts with 3-carboxybenzophenone moiety, resulting from radical recombination reaction. Another identified product formed during photolysis was 3CB-3CB benzpinacol photoadduct, which has similar structure to the product of BP irradiations. Identified products (MetSO and the photo-adduct) were formed from the α-S via disproportionation or reaction with 3CBH•/3CBH•⁻. The oxidation of Met-Lys-Bradykinin (MKBR) yielded formation of similar photo-adducts via sensitized reaction with the 3CB*. The •OH induced oxidation of MKBR yielded several products, e.g. the sulfoxide and hydroxylated phenylalanine. In addition, other derivatives of benzophenone (oxybenzone (OXB) and sulisobenzone (SB)) were investigated due. They are widely used in commercial sun-protecting products dp to their unique photophysical properties. However the application of sunscreens awakes controversies because some epidemiological studies indicated an increased risk of malignant melanoma for their users. Photo-instability of sunscreen filters would result in reduced protection and may produce reactive free radicals or mutagens. In addition, the reactions of the sunscreens with oxygen free radicals e.g. hydroxyl radicals are likely to arise and they were not yet sufficiently documented. Finally, the radiolytic and photolytic properties of SB and OXB were investigated using femto-and nanosecond laser flash photolysis. Pulse radiolysis studies of the oxidation of those molecules by •OH radicals were performed. The results obtained for SB and OXB were compared to several other benzophenone derivatives. The results shown the formation of excited singlet state that was deactivated efficiently via the Excited State Intramolecular Proton Transfer (ESIPT). In case of polar solvent, the formation of trace amounts phenoxyl radicals was identified, while for nonpolar media those radicals were not observed. The reactivity of UV-excited sun filters towards simple derivatives of Met was also investigated, however, this topic requires further and more detailed investigations.

Processes at the air-water/ice interface are known to play a very important role in the release of reactive halogen species with atmospheric aerosols serving as catalysts. The ability to make different types of ice with various morphologies, hence, different adsorption and surface properties in vacuum, provide a useful way to probe the catalytic effect of ice in atmospheric reactions. Also, the use of the liquid jet technique provides the rare opportunity to probe liquid samples at the interface; hitherto impossible to investigate with traditional surface science techniques. Studies of reactions on both ice and liquid surfaces at ambient conditions are usually complicated by the rapid desorption and adsorption processes due to the high evaporation rates at the surface. To gain a better understanding and improve modeling of several atmospheric relevant reactions, it is therefore important to develop laboratory techniques that provide an opportunity to investigate non-thermal reactions on both ice and liquid surfaces. Detailed investigation of the interactions of atmospheric relevant molecules (methyl iodide and hydrogen chloride) on water ice at low temperature in UHV conditions has been carried out. These interactions were studied using different techniques such as temperature programmed desorption (TPD), electron stimulated desorption (ESD) and resonance enhanced multiphoton ionization (REMPI). Unlike probing reactions on ice surfaces, investigating air/liquid interfaces present several challenges. This is because traditional surface science techniques require an ultra high vacuum environment to prevent distortion of information due to interference from equilibrium vapor above the liquid surface during data acquisition. The liquid jet technique facilitates the direct study of continually renewed liquid surfaces in high vacuum, thereby preventing the constant changing of the properties and composition of the liquid surface due to the aging process (diffusion of impurities or liquid constituent). A linear time-of-flight mass spectrometer has been used to monitor ion ejection during laser irradiation of liquid jet containing aqueous solutions and pure water. Since these ions are ejected exclusively from the surface of the liquid and the cluster distributions observed are influenced by the local structure, these experiments provide a sensitive probe of the liquid vacuum interface of these solutions. Though the research is fundamental, the results obtained from these investigations indicate how the discontinuity of bulk properties on the surface of both ice and aqueous solutions affects interfacial reactions.

Many anticancer therapies are based on the interaction of small molecule drugs with nucleic acids, particularly DNA. Electrospray ionization tandem mass spectrometry has established itself as an irreplaceable tool for the characterization of DNA adducts produced by alkylating agents, carcinogens, and antitumor drugs, in addition to the characterization of nucleic acid post-transcriptional modifications. ESI-MS was used to assess the non-covalent binding of a novel series of intercalating anthrapyrazoles to duplexes containing different sequences. Relative binding affinities paralleled the shift in melting point of the DNA duplexes measured from a previous study. Upon collisionally induced dissociation of the duplex/anthrapyrazole complexes, different binding strengths were discerned based on the fragmentation patterns. In addition, the interactions of a new series of sulfur-containing acridine ligands, some that functioned as alklyating mustards, with duplex DNA were also evaluated. Non-covalent and covalent binding of each ligand was determined, and the site of adduction (G > A) was revealed for the covalent modifications. The distribution of cross-linked products and mono-adducts by psoralen analogs was also monitored by both LC-UV and IRMPD-MS methods. Reactions at 5’-TA sites were favored over 5’-AT sites. The sites of interstrand cross-linking were determined by fragmentation of the duplex/psoralen complexes by infrared multiphoton dissociation (IRMPD). Ultraviolet photodissociation (UVPD) at 193 nm caused efficient charge reduction of deprotonated oligodeoxynucleotides via electron detachment. Subsequent CID of the charge-reduced oligodeoxynucleotides formed upon electron detachment, in a net process called electron photodetachment dissociation (EPD), resulted in a diverse array of abundant sequence ions which allowed the modification site(s) of three modified oligodeoxynucleotides to be pinpointed to a more specific location than by conventional CID. Electron transfer dissociation (ETD) caused efficient charge reduction of multi-protonated oligonucleotides. Subsequent CAD of the charge-reduced oligonucleotides formed upon electron transfer, in a net process termed electron transfer collision activated dissociation (ETcaD), resulted in rich backbone fragmentation, with a marked decrease in the abundance of base loss ions and internal fragments. ETcaD of an oligonucleotide duplex resulted in specific backbone cleavages, with conservation of weaker non-covalent bonds. In addition, IRMPD and UVPD were used to activate charge-reduced oligonucleotides formed upon electron transfer. ET-IRMPD afforded tunable characterization of the modified DNA and RNA, allowing for modified bases to be directly analyzed. ET-UVPD promoted higher energy backbone fragmentation pathways and created the most diverse MS/MS spectra. The numerous products generated by the hybrid MS/MS techniques (ETcaD, ET-IRMPD, and ET-UVPD) resulted in specific and extensive backbone cleavages which allowed for the modification sites of multiple oligonucleotides to be pinpointed. / text