The functional and pathogenic roles of biomolecules are often coupled to the self-association of their basic units into oligomers and aggregates whose structural details are difficult to distinguish because of their insoluble and heterogenous nature. This work focuses on DNA G-quadruplex motifs and amyloid peptides whose oligomers and aggregates are associated with numerous biological roles and human diseases. Infrared (IR) spectroscopy is a powerful tool which probes vibrational transitions whose signatures report on their arrangement within molecules. Advances in two-dimensional infrared (2D IR) spectroscopy have allowed structural characterization in increasingly complex biomolecules that are not amenable to traditional high-resolution techniques. However, careful consideration of the physical phenomena that lead to IR spectra are necessary to make accurate assignments. In the first portion of this work, using FTIR and 2D IR, we determine spectral markers that can differentiate size, metal ion coordination, and topology in DNA G-quadruplex motifs. IR studies aided by isotope labeling define the physical origin of these markers and allow for the construction of a structural landscape in parallel DNA G-quadruplex motifs. It is also shown that 2D IR and isotope editing probes site-specific structural changes in G-quadruplex motifs that can differentiate ion identity and location based on spectral shifts. In the latter portion of this work, we use a combination of spectroscopy and imaging techniques to show that a peptide derived from the human pro-apoptotic protein BAX forms amyloid aggregates whose structure is dependent on the presence of model membranes. Combined, the work in this thesis allows for the formulation of multiple hypotheses based on IR structural assignments regarding disease states and functional mechanisms of these systems.

京都大学 / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第19415号 / エネ博第323号 / 新制||エネ||65(附属図書館) / 32440 / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 片平 正人, 教授 森井 孝, 教授 木下 正弘 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第19527号 / 理博第4187号 / 新制||理||1601(附属図書館) / 32563 / 京都大学大学院理学研究科化学専攻 / (主査)教授 杉山 弘, 教授 三木 邦夫, 教授 藤井 紀子 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

The treatment and/or prevention of cancer by selective down regulation of cancer causing gene (oncogene) transcription would represent a significant advance in the area of anticancer drug design. Non-canonical higher order DNA structures formed in oncogene promoter regions are novel targets for the modulation of oncogene expression. An obvious advantage of selectively targeting oncogene expression would be that general cytotoxicity would be minimized and the negative side effects of current chemotherapy approaches could be minimized or eliminated. To provide a foundation for the design of drugs that target oncogene promoter G-quadruplexes and i-Motifs, the basic understanding is required of the folding of guanine and cytosine rich sequences and how small molecules bind to these structures. The research reported here focuses on higher order DNA structures of two oncogenes, K-ras that is overexpressed in pancreatic cancer, and Bcl-2 that is overexpressed in a number of cancers, and one non-oncogene, HAR1. We have probed the overall structure, stability, and binding of a model drug compounds to G-quadruplex and i-Motif DNA structures in these genes. The overall objectives of this work were: 1) to understand the relationship between oligonucleotide sequence and intramolecular folding topology and stability, and 2) to understand the mechanisms for the selective binding of small molecules to these structures. Biophysical techniques including: microcalorimetry, spectroscopy, analytical ultracentrifugation, gel electrophoresis, and computational methods were used to characterize both the folding and the binding interactions. We have shown that the native K-ras purine and pyrimidine rich sequences form stable G-quadruplexes and i-Motifs. We have also characterized four G-rich sequences found within the reading frame of the human HAR1 gene. This is the first report on the formation of stable G-quadruplex motifs within the RF of any gene. The model drug, TMPyP4, binds to the Bcl-2, K-ras, and HAR1 G-quadruplexes by two different binding modes, end binding and intercalation. The significance of this research is that the results of the K-ras and Bcl-2 studies could lead to the design of drugs that selectively target oncogenes while the HAR1 results could provide new approaches to the treatment of Schizophrenia and Alzheimer’s disease.

Squaraine dyes have attracted more attention in the past decade due to their strong and narrow absorption and fluorescence along with the easily functionalized molecular structure. One successful approach of core functionalization is to replace one oxygen of the squaric carbonyl group with a dicyanomethylene group, which shifts the absorption and emission into the near infrared (NIR) region and at the same time leads to a rigid, planar structure with C2v symmetry. However, such squaraines tend to aggregate cofacially in solution due to dispersion forces and dipole-dipole interactions, usually leading to H-type exciton coupling with undesired blue-shifted spectrum and quenched fluorescence. Therefore, the goal of my research was the design of dicyanomethylene-substituted squaraine dyes that self-assemble into extended aggregates in solution with J-type coupling, in order to retain or even enhance their outstanding optical properties. Toward this goal, bis(squaraine) dyes were envisioned with two squaraine units covalently linked to trigger a slip-stacked packing motif within the aggregates to enable J-type coupling. In my first project, bis(squaraine) dye BisSQ1 was synthesized, in which two dicyanomethylene squaraine chromophores are covalently linked. Concentration and temperature-dependent UV/Vis/NIR spectroscopy experiments reveal that BisSQ1 undergoes cooperative self-assembly resulting in J-type aggregates in a solvent mixture of toluene/1,1,2,2-tetrachloroethane (TCE) (98:2, v/v). The J type exciton coupling is evident from the significantly red shifted absorption maximum at 886 nm and the fluorescence peak at 904 nm. In conclusion, this was a first example to direct squaraine dye aggregation in solution to the more desired slip-stacked packing leading to J-type exciton coupling by simply connecting two dyes in a head-to-tail bis chromophore structure. Connecting two squaraine dyes with an additional phenylene spacer (BisSQ2) leads to two different polymorphs with very distinct absorption spectra upon cooling down a solution of BisSQ2 in a solvent mixture of toluene/TCE (98:2, v/v) with different rates. Accordingly, rapid cooling resulted in rigid helical nanorods with an absorption spectrum showing a panchromatic feature, while slow cooling led to a sheet-like structure with a significant bathochromic shift in the absorption spectrum. It was discovered that the conventional molecular exciton model failed to explain the panchromatic absorption features of the nanorods for the given packing arrangement, therefore more profound theoretical investigations based on the Essential States Model (ESM) were applied to unveil the importance of intermolecular charge transfer (ICT) to adequately describe the panchromatic absorption spectrum. Moreover, the red-shift observed in the spectrum for the sheet-like structure can be assigned to the interplay of Coulomb coupling and ICT-mediated coupling. Furthermore, the same bis-chromophore strategy was adopted for constructing an NIR-II emitter with a bathochromically-shifted spectrum. In chloroform, BisSQ3 exhibits an absorption maximum at 961 nm with a significant bathochromic shift (1020 cm−1) compared to the reference mono-squaraine SQ, indicating intramolecular J-type coupling via head-to-tail arrangement of two squaraine dyes. Moreover, BisSQ3 shows a fluorescence peak at 971 nm with a decent quantum yield of 0.33%. In less polar toluene, BisSQ3 self-assembles into nanofibers with additional intermolecular J-type coupling, causing a pronounced bathochromic shift with absorption maximum at 1095 nm and a fluorescence peak at 1116 nm. Thus, connecting two quinoline-based squaraines in a head-to-tail fashion leads to not only intra-, but also intermolecular J-type exciton coupling, which serves as a promising strategy to shift the absorption and emission of organic fluorophores into the NIR-II window while retaining decent quantum yields. In conclusion, my research illustrates based on squaraine dyes how a simple modification of the molecular structure can significantly affect the aggregation behavior and further alter the optical properties of dye aggregates. Elongated supramolecular structures based on dicyanomethylene substituted squaraine dyes were successfully established by covalently linking two squaraine units to form a bis-chromophore structure. Then, a simple but efficient general approach was established to direct squaraine dye aggregation in solution to the more desired slip-stacked packing leading to J-type exciton coupling by directly connecting two squaraine dyes in a head-to-tail fashion without spacer units. Moreover, the additional spacer between the squaraine dyes in BisSQ2 allowed different molecular conformations, which leads to two different morphologies depending on the cooling rates for a hot solution. Hence, this is a promising strategy to realize supramolecular polymorphism. In general, it is expected that the concept of constructing J-aggregates by the bis-chromophore approach can be extended to entirely different classes of dyes since J-aggregates possess a variety of features such as spectral shifts into the NIR window, fluorescence enhancement, and light harvesting, which are commonly observed and utilized for numerous fundamental studies and applications. Moreover, the insights on short-range charge transfer coupling for squaraine dyes is considered of relevance for all materials based on alternating donor-acceptor π-systems. The panchromatic spectral feature is in particular crucial for acceptor-donor-acceptor (ADA) dyes, which are currently considered as very promising materials for the development of bulk heterojunction solar cells. / Squarainfarbstoffe haben in den letzten Jahren aufgrund ihrer hervorragenden optischen Eigenschaften, zu denen ein Cyanin-ähnliches Absorptions- und Fluoreszenzverhalten zählt, in Kombination mit einer leicht funktionalisierbaren Molekülstruktur immer mehr Aufmerksamkeit auf sich gezogen.22 Ein erfolgreicher Ansatz der Kernfunktionalisierung besteht darin, ein Sauerstoffatom der Quadratsäure-Carbonylgruppe durch eine Dicyanomethyleneinheit zu ersetzen, was die Absorption und Emission in den nahen infraroten (NIR-) Bereich verschiebt und gleichzeitig zu einer starren planaren Struktur mit C2v Symmetrie und einem Grundzustandsdipolmoment führt.27 Diese Eigenschaften haben sich als vorteilhaft für die π-π-Aggregation von diesen Squarainen auf G-Quadruplex (G4) Strukturen erwiesen, wie in Kapitel 6 beschrieben. Solche Squaraine neigen jedoch zur Bildung von Dimeren oder kleinen Aggregaten in Lösung mit kofazialen Chromophoranordnungen aufgrund Dispersionskräften und Dipol-Dipol-Wechselwirkungen. Dies resultiert in der Regel zu einer H-artigen exzitonischen Kopplung mit unerwünschten, blauverschobenen Absorptionsbanden und gelöschter Fluoreszenz.28 Daher war das Ziel dieser Dissertation, Dicyanomethylen-substituierte Squarainfarbstoffe zu entwickeln, die sich in Lösung zu verlängerten Aggregaten mit J-artiger Kopplung selbst organisieren. Auf diese Weise sollten die ausgezeichneten optischen Eigenschaften der Squarainfarbstoffe erhalten oder sogar verbessert werden. Zu diesem Zweck, wurden Bis(squarain)-Farbstoffe synthetisiert, in denen zwei Squarain-Einheiten kovalent verbunden sind, was zu einer gestapelten Anordnung mit longitudinalem Versatz innerhalb der Aggregate und damit zu einer J-artigen Kopplung führt. ...

<p>c-Myc is one of the most important oncogenes. G-quadruplex DNA secondary structure formed in the proximal promoter region of c-Myc functions as a transcription silencer and is targetable by small molecules. Therefore, the c-Myc promoter G-quadruplex (MycG4) is an attractive anticancer drug target. Protein recognition of MycG4 is essential for its transcriptional regulating. Nucleolin was discovered as a major MycG4 binding protein in 2009. It shows a remarkably higher binding affinity for MycG4 over its known substrate NRE_RNA and overexpression of nucleolin represses the activity of the c-Myc promoter. However, little is known about its molecular recognition of MycG4. Here, we use X-ray crystallography combined with other biochemical and biophysical methods to understand how nucleolin recognizes MycG4. Nucleolin is a 77 kD protein with a modular organization. The four RNA-binding domains (RBD) of nucleolin are the minimal domains for high affinity binding with MycG4. We show that nucleolin prefers the c-Myc parallel G-quadruplex with a 6-nt central loop (Myc161) that is the thermodynamically favored conformation. Using a custom G4 DNA microarray, we optimized the MycG4 sequence with over 10-fold increased binding affinity to nucleolin. Fabs are widely used tools to facilitate crystallization and we have discovered Fabs that specifically bind the nucleolin-MycG4 complex using a phage display screening. This approach enabled us to obtain crystals of the nucleolin-MycG4-Fab ternary complex diffracted at 2.6 Å and we determined the crystal structure. In the structure, the parallel MycG4 is very well-defined with two K⁺ between the three G-treads. The central 6-nt loop residue protrude from the G4-core and extensively recognized by the nucleolin. Only RBD1 and RBD2 of nucleolin are seen in the crystal structures and interact extensively with the 6-nt central loop and 5′-flanking of MycG4. The binding surface and area of the globular MycG4 by nucleolin is much more extensive than NRE_RNA and involves an extra binding site. Fab binds to both RBD1 and 3′-end of MycG4 to stabilize the complex. The well-defined partial RBD2-3 linker and a cavity close to the 1-nt T19 loop suggest that the missing RBD3 likely binds the 3^rd loop of MycG4. This structure is the first MycG4-protein complex structure. It will help understand MycG4 and nucleolin interactions and the development of MycG4 targeted cancer therapeutics. This structure also provides novel insights into how proteins recognize the globular G-quadruplexes, highlighting the potential of G-quadruplexes as a platform for multivalent interactions such as with multiple tandem RBDs.</p>

京都大学 / 新制・課程博士 / 博士(医科学) / 甲第24805号 / 医科博第150号 / 新制||医科||10(附属図書館) / 京都大学大学院医学研究科医科学専攻 / (主査)教授 生田 宏一, 教授 上野 英樹, 教授 濵﨑 洋子 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

The objective of this project was to develop a DNA hybridization sensor that can detect the presence of E. coli and reveal its resistance to the drug gentamicin. This probe will enable rapid and user-friendly diagnostics of E. coli infections and analysis of bacterial gentamicin-susceptibility profile by interrogation of a fragment of E. coli 16S rRNA bearing a substitution in the gentamicin-resistant cells. The sensor is promising for the point-of-care use to provide a timely UTI diagnostic solution. A quick diagnosis of E. coli infection and antibiotic resistance is crucial for treatment. To design a hybridization probe, we proposed a split approach for target interrogation and catalytic activity of a peroxidase-like deoxyribozyme (PDz) as a signal reporter. PDz contains a series of guanine residues in a strand and has been shown to form a parallel guanine-quadruplex (G4). This G4, with the addition of a hemin cofactor, catalyzes the reaction similar to that of horseradish peroxidase. If a colorless organic indicator is added to the G4-PDz-hemin containing solution and mixed H2O2, a colored oxidation product is formed (e.g., a dark blue/green). The color change reports the presence of the catalytically active G4, which occurs only when the nucleotide sequence of the target is a perfect match. When the target is not a perfect match, for example, in the case of the drug-causing nucleotide substitution, the G4 does not form, and there is no color change. The probes tested in this paper show promising results of such a sensor by being able to catalyze the described colorimetric reaction to generate a strong signal in the presence of a "gentamicin-susceptible" target and show selectivity against the "gentamicin-resistant" target.

No description available.