DNA photocleaving reagents are a unique class of molecules that display the ability to cleave DNA, causing strand breaks, upon exposure to an irradiation source. In terms of biological applications, achieving excitation through a two-photon absorption event provides for unique benefits that can be useful in such applications as photodynamic therapy and cell viability studies. Thus, this thesis pertains to the study of a class of photocleaving reagents that have been shown to become excited through a twophoton process during irradiation with a pulsed femtosecond laser at 775 nm. N-(Alkoxy)pyridinethiones were selected as possible oxygen-based radical generators upon irradiation at two-photon wavelengths. Experiments were carried out with pBR 322 plasmid DNA to determine if these N-(alkoxy)pyridinethiones could cause strand cleavage and if so how efficient they are in doing so. Several compounds were found to be effective DNA strand cleavers when irradiated at two-photon wavelengths, displaying the utility of two-photon excitation in biological studies. Rationale is suggested for the observed variation in cleaving efficiency based on inherent properties of the generated radicals. A second study was done to measure the two-photon cross section of the compound N-(anthracenoyloxy)pyridinethione. The two-photon cross section was found by measuring the fraction of substrate remaining after specific periods of femtosecond laser irradiation at 775 nm, and the two-photon cross section was found to be 0.051 GM.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22301号 / 医博第4542号 / 新制||医||1040(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 渡邊 直樹, 教授 椛島 健治, 教授 林 康紀 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

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Fluorescence microscopy allows for spatial and temporal resolution of systems which are inherently fluorescent or which can be selectively labeled with fluorescent molecules. Temporal resolution is crucial for imaging real time processes in living samples. A common problem in fluorescence microscopy of biological samples is autofluorescence, fluorescence inherent to the system, which interferes with detection of fluorescence of interest by decreasing the signal to noise ratio. Two current methods for improved imaging against autofluorescence are two-photon excitation and total internal reflection microscopy. Two-photon excitation occurs when two longer wavelength photons are absorbed quasi-simultaneously by a single fluorophore. For this to take place there must be a photon density on the order of 1030 photons/(cm2)(s), which is achieved through use of a femtosecond pulsed laser and a high magnification microscope objective. Two-photon excitation then only occurs at the focal spot, significantly reducing the focal volume and therefore background autofluorescence. The second method, total internal reflection, is based on evanescent wave excitation, which decreases exponentially in intensity away from the imaging surface. This allows for excitation of a thin (~200 nm) slice of a sample. Since only a narrow region of interest is excited, an optical slice can be imaged, decreasing excitation of out-of-focus autofluorescence, and increasing the signal to noise ratio. By coupling total internal reflection with two-photon excitation, an entire cell can be imaged while still maintaining the use of lower energy photons to irradiate the sample and achieve two-photon excitation along the length traveled by the evanescent wave. This system allows for more sensitive detection of fluorescence of interest from biological systems as a result of a significant decrease in excitation volume and therefore a decrease in autofluorescence signal. In the two-photon total internal reflection microscopy setup detailed in this work, an excitation area of 20 μm by 30 μm is achieved, and used to image FITC-stained actin filaments in BS-C-1 cells

Fluorescence-based techniques are widely used in bioscience, offering a high sensitivity and versatility. In this work, fluorescence electronic energy migration/ transfer is applied to measure intramolecular distances in two types of systems and under various conditions. The main part of the thesis utilizes the process of donor-acceptor energy transfer to probe distances within the ribosomal protein S16. Proteins are essential to all organisms. Therefore, it is of great interest to study protein structure and function in order to understand and prevent protein malfunction. Moreover, it is also important to try to study the proteins in an environment which resembles its natural habitat. Here two protein homologs were investigated; S16Thermo and S16Meso, isolated from a hyperthemophilic bacterium and a mesophilic bacterium, respectively. It was concluded that the chemically induced unfolded state ensemble of S16Thermo is more compact than the corresponding ensemble of S16Meso. This unfolded state compaction may be one reason for the increased thermal stability of S16Thermo as compared to S16Meso. The unfolded state of S16 was also studied under highly crowded conditions, mimicking the environment found in cells. It appears that a high degree of crowding, induced by 200 mg/mL dextran 20, forces the unfolded state ensemble of S16Thermo to become even more compact. Further, intramolecular distances in the folded state of five S16 mutants were investigated upon increasing amounts of dextran 20. We found that the probed distances in S16Thermo are unaffected by increasing degree of crowding. However, S16Meso shows decreasing intramolecular distances for all three studied variants, up to 100 mg/mL dextran. At higher concentrations, the change in distance becomes anisotropic. This suggests that marginally stable proteins like s16Meso may respond to macromolecular crowding by fine-tuning its structure. More stable proteins like S16Thermo however, show no structural change upon increasing degree of crowding. We also investigated the possibility of local specific interactions between the protein and crowding agent, by means of fluorescence quenching experiments. Upon increasing amounts of a tyrosine labelled dextran, a diverse pattern of fluorescence quantum yield and lifetime suggests that specific, local protein-crowder interactions may occur. In a second studied system, electronic energy migration between two donor-groups, separated by a rigid steroid, was studied by two-photon excitation depolarization experiments. Data were analysed by using recent advances, based on the extended Förster theory, which yield a reasonable value of the distance between the two interacting donor-groups. To the best of our knowledge, this is the first quantitative analysis of energy migration data, obtained from two-photon excited fluorescence.

This dissertation is author version of following the journal article. Rei Mizuno, Yuji Kamioka, Kenji Kabashima, Masamichi Imajo, Kenta Sumiyama, Eiji Nakasho, Takeshi Ito, Yoko Hamazaki, Yoshihisa Okuchi, Yoshiharu Sakai, Etsuko Kiyokawa, and Michiyuki Matsuda. "In vivo imaging reveals PKA regulation of ERK activity during neutrophil recruitment to inflamed intestines" J Exp Med 2014 211:1123-1136. Published May 19, 2014, doi:10.1084/jem.20132112 / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18542号 / 医博第3935号 / 新制||医||1006(附属図書館) / 31442 / 京都大学大学院医学研究科医学専攻 / (主査)教授 岩井 一宏, 教授 千葉 勉, 教授 長澤 丘司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Nanoscale materials have great applications in many areas. One of these applications is for manufacturing ultra-compact and efficient sensors for chemical and biological molecule detection. Noble metals, such as gold (Au) and silver (Ag), because of their distinguished optical property"localized surface plasmon resonances (LSPRs) that exhibit low loss, are ideal materials to fabricate these nanoscale plasmonic particles or structures. This work addresses the synthesis, characterization, and sensing applications of Au and Ag nanoparticles (NPs). The progress on certain subjects related to our work"NP synthesis, surface functionalization, Au sphere-film structure and two-photon fluorescence"are reviewed in Chapter 1. We also show the calculation results of LSPRs of Au nanosphere suspensions using Mie theory. The measured extinction spectra of Au nanosphere suspensions agree with the calculated results very well. Chapter 2 is a chapter describing the chemical synthesis of a variety of NPs, such as Ag prisms and cubes, Au spheres, rods, and bipyramids. These experiments involved different synthetic mechanisms and methods which enabled us to prepare NPs with desired shapes and optical properties. To put these NPs into application, it is desirable and sometimes necessary to functionalize their surfaces. In Chapter 3, we present the functionalization of Ag cubes with poly(allylamine hydrochloride) (PAH) and poly(allylamine hydrochloride)-dithiocarbamate (PAH-DTC), which follows our previous work on Au NPs. The purpose of studying Ag instead of Au is to use the stronger plasmonic enhancement in Ag when applied to two-photon imaging applications. However, we found that PAH-DTC shrank the Ag cubes. We also functionalized the cationic hexadecyltrimethylammonium bromide (CTAB)-stabilized Au NRs with anionic poly(sodium 4-styrenesulfonate) (PSS). Coated with the strong polyelectrolyte PSS, the NRs become more manageable and can be stable for over six months and are easily immobilized onto positively charged substrate. We put PSS-functionalized Au NPs into use and studied their adsorption process onto PAH-coated optical fiber tapers by monitoring the transmission light through the fiber. When the diameter of the fiber taper gets smaller, stronger coupling occurred between transmitted light inside the taper and the Au NPs on the taper surface (cylinder). This coupling resulted in a loss of the guided light at the plasmon resonance wavelength of the NPs. By monitoring this loss, we can study the adsorption rate of Au NPs onto the fiber. In Chapter 4, we used Au nanospheres to study the adsorption rate on substrates with different curvatures. We also established a theoretical model to explain this phenomenon for cylindrical surface as well as planar and spherical surfaces. Our results fit well with the theory, which predicts that particle adsorption rates depend strongly on surface geometry, and can exceed the planar surface deposition rate by over two orders of magnitude when the diffusion length of the particle is large compared to the surface curvature. In Chapter 5, we studied the optical properties of Au nanospheres separated from a thick Au film by a polyelectrolyte multilayer (PEM) film assembled from PAH and PSS under specific pH condition. The PEM film undergoes swelling and shrinking when the environmental pH is changed as a result of charging and discharging of the polyelectrolytes. Therefore, the PEM film provides an efficient means to tune the distance between Au spheres and Au film. The extinction peak blue-shifted as much as 100 nm when the pH of the water changed from pH 10 to pH 3 for 100 nm diameter Au spheres on a PEM film assembled at pH 9.5. Our preliminary estimates that the gap between sphere and surface can be as small as a few nm even though the film itself is tens of nm thick when it is not constrained by Au spheres. We studied two-photon excitation fluorescence (TPEF) from Ag triangles in Chapter 6. The triangles were fabricated by nanosphere lithography, which used convective self-assembly to make the nanosphere mask. The LSPRs of the nanotriangles were tuned to be in the 800--900 nm range to match with the Ti:Sapphire pulse laser at 880 nm. We found that certain spots on the fluorescence images gave rise to larger fluorescence intensity than rest of the area. SEM imaging reveals that the unusually bright spots seen on the surface were related to regions where the triangles transformed to spherical particles. The larger intensity is tentatively ascribed to the plasmon resonance of those spherical particles in ~400 nm range. / Ph. D.

Gold nanoparticles (GNP) have been widely used as optical imaging and photothermal therapy agents due to their biocompatibility, simplicity of conjugation chemistry, optical tunability and efficient light conversion to heat. A number of in vitro and in vivo studies have demonstrated that they can be used as effective thermal therapy and imaging contrast agents to treat and diagnose cancer. As clinical applications of GNPs for cancer imaging and therapy have gained interest, efforts for understanding their accumulation kinetics has become more important. Given the recent demonstration of intrinsic two-photon induced photoluminescence (TPIP) of gold nanoshells (GNSs) and gold nanorods (GNRs), TPIP imaging is an efficient tool for investigating the microscopic distribution of the GNPs at intra-organ level. The following work explores these GNPs’ physical and optical properties for effective use of GNPs in TPIP imaging and examines the feasibility of using intrinsic TPIP imaging to investigate GNP’s biodistribution in bulk tumors and thin tissue slices processed for standard histology. Our results showed that GNPs yield a strong TPIP signal, and we found that the direct luminescence-based contrast imaging of GNPs can image both GNPs and nuclei, cytoplasm or vasculature simultaneously. Also, we present the effect of GNP morphology on their distribution within organs. Collected images showed that GNPs had a heterogeneous distribution with higher accumulation at the tumor periphery. However, GNRs had deeper penetration into tumor than GNRs due to their shape and size. In addition, GNPs were observed in unique patterns close to vasculature. Finally, we introduce single- and multiple-dose administrations of GNPs as a way of increasing GNP accumulation in tumor. Our results show that multiple dosing can increase GNP accumulation in tumor 1.6 to 2 times more than single dosing. Histological analysis also demonstrated that there were no signs of acute toxicity in tumor, liver and spleen excised from the mice receiving 1 injection, 5 injections of GNPs and trehalose injection. / text

Fluorescent nucleic acid base analogues (FBAs) are an important class of molecule used to study the structure and dynamics of DNA and RNA. These base analogues are molecules with structures that resemble one of the natural bases but which, unlike the natural bases, have high fluorescence quantum yields. 2-Aminopurine (2AP) has long been the most widely used fluorescent base analogue and is one of the few base analogues commercially available. One problem with 2AP is that it undergoes significant quenching when incorporated into DNA: the quantum yield decreases 100 fold from that of the free base, thus becoming too low for use in, for example, single molecule studies. A secondary problem is that the 305 nm absorption peak requires excitation in the UV. A variety of new fluorescent base analogues are being produced, with a view to remedying the deficiencies of 2AP and expanding the current range of use. The first part of this thesis explores the one-photon photophysical properties of several of these novel FBAs. The first of these novel FBAs is the 6-aza-uridine family. These compounds, analogues of uridine, have large Stokes shifts and their absorption and emission spectra are red-shifted in comparison to 2AP; their quantum yields as free bases have been shown to exceed that of 2AP and their environmental sensitivity has been demonstrated. Time-resolved measurements reported in this thesis indicate the presence of multiple emitting species. A density functional theory (DFT) study has been carried out to rationalise these emitting species as rotational isomers. Similar fluorescence lifetime measurements were made on a second class of FBAs, the quadracyclic adenine analogues, qANs; these results also indicated the presence of multiple emitting species. Experimental results show that these FBAs undergo excited-state proton transfer. The final FBA studied in this thesis is pentacyclic adenine, pA. This FBA showed some of the most promising characteristics of all the analogues investigated, such as a high quantum yield in both polar and non-polar solvents. A time-resolved investigation into pA-containing oligonucleotides indicated that in an oligonucleotide pA adopts multiple stacked conformations and its behaviour is highly sequence dependent. Several of these aforementioned fluorescent base analogues have absorption spectra in a region that makes them accessible to two-photon (2P) excitation with a Ti:Sapphire laser. In biological systems, multiphoton excitation has several advantages over one-photon excitation. By avoiding the use of ultraviolet light there is reduced phototoxicity. Out of focus photobleaching and autofluorescence are also minimised which leads to a higher signal-to-background ratio and allows deeper tissue penetration to be achieved. Fluorescent base analogues tend to have small Stokes shifts; this is another problem that can be overcome by using two-photon excitation. To be of potential use in multiphoton microscopy, a FBA must have a high two-photon absorption cross-section and a high two-photon brightness. Previously, the highest two- photon brightness measured for a fluorescent base analogue was less than 2 GM. Amongst the base analogues investigated here, are several that have higher two-photon brightness than ever reported for FBAs; these include pA which is shown to have the highest 2P brightness of a FBA in an oligonucleotide, 1.3 GM, and a member of the 6-azauridine family which as a free base has a 2P brightness of 18 GM. Detection of individual molecules represents the ultimate level of sensitivity and enables details about a molecular system that would otherwise be concealed using conventional ensemble techniques to be revealed. With the improved 2P brightness of the molecules measured in this thesis, it has become feasible to detect single FBA molecules using 2P excitation. To maximise the chance of detection, ultrafast, shaped laser pulses have been used as the excitation source. For the first time, the signal has been high enough and the molecule of interest sufficiently photostable such that 2P fluorescence correlation spectroscopy of a fluorescent base analogue in an oligonucleotide could be measured. In summary, this thesis reports the fluorescence lifetimes and two-photon cross-sections of a series of novel fluorescent base analogues, as well as fluorescence correlation spectroscopy measurements of the most promising candidates.

A new and general procedure is described for a detailed analysis of time-resolved fluorescence depolarisation data in the presence of electronic energy migration. An isotropic ensemble of bifluorophoric molecules (D1-R-D2) has been studied to demonstrate its utility. Intramolecular donor-donor energy migration occurs between the two donor groups (D), which are covalently connected to a rigid linker group (R). These groups undergo restricted reorientational motions with respect to the R group. The analysis of depolarisation data basically involves the search for best-fit parameters which describe the local reorienting motions, the interfluorophore D1-D2 distance, as well as the mutual orientations of the donors. For this, the analysis is partly performed in the Fourier domain and the best-fit parameters are determined by using an approach based on a Genetic Algorithm. The energy migration process has been described by using Monte Carlo simulations and an extended Förster theory. It is found that this theory provides the least time-consuming computational method. Since one-photon and two-photon excited fluorescence experiments can be applied for energy migration studies, a general and unified theoretical formulation is given. To exemplify the developed quantitative approach the depolarisation of the fluorescence in the presence of electronic energy migration within a bis-(9-anthrylmethylphosphonate) bisteroid molecule has been studied by time-resolved two-photon excited fluorescence depolarisation experiments. To solely obtain information about local reorientations of the 9-anthrylmethyl group, also the mono-(9-anthrylmethylphosphonate) bisteroid was studied, which enabled modelling of the ordering potential of the donor. Values of the two-photon absorption tensor components were obtained. To describe the discrepancy between the measured values of the initial anisotropy and fundamental anisotropy predicted by theory the distribution of absorption tensor caused by fast processes have been introduced. An angular parameter of absorption tensor was determined. Reasonable values of the distance between the 9-anthrylmethyl groups, as well as for their mutual orientation were obtained.