A series of polypeptides with well-defined sequences, (Asp3Phe1)n, (Asp2Phe1)n, (Asp1Phe1)n, (Asp1Phe2)n, and (Asp1Phe3)n, containing the hydrophilic amino acid, aspartic acid (Asp) and the hydrophobic amino acid, phenylalanine (Phe), were synthesized. Their behaviour in aqueous solution was investigated by performing fluorescence quenching and non-radiative energy transfer (NRET) experiments which were complemented by dynamic (DLS) and static (SLS) light scattering. The photophysical properties of the polypeptides were dependent on their Phe content. An increase in the Phe content led to an increase in the extinction coefficient, fluorescence quantum yield, and fluorescence average lifetime of the polypeptides. Circular dichroism experiments revealed that except for the (Asp1Phe3)n polypeptide, which adopts an alpha-helical conformation in aqueous solution, the other polypeptides did not adopt any known conformation in solution. The fluorescence quenching studies performed using molecular pyrene physically bound to the polypeptide via hydrophobic interactions resulted in protective quenching for the (Asp1Phe1)n, (Asp1Phe2)n, and (Asp1Phe3)n polypeptides, with some pyrenes having a lifetime of ~300 ns. Evidence for protective quenching was also observed in the polypeptides richer in Phe, when pyrene was covalently attached onto the polypeptides. However pyrene was found to be fully exposed to the quencher solution for the more hydrophilic polypeptides. The presence of NRET between a naphthalene labeled polypeptide and a pyrene labeled polypeptide for the (Asp1Phe2)n and (Asp1Phe3)n polypeptides and its absence for the (Asp3Phe1)n, (Asp2Phe1)n, and (Asp1Phe1)n polypeptides led to the conclusion that those polypeptides richer in Phe generate interpolymeric aggregates which provide protection to a hydrophobic cargo like molecular pyrene whereas the hydrophilic polypeptides exist predominantly as unimolecular micelles. These results were confirmed by DLS and SLS experiments.

A series of polypeptides with well-defined sequences, (Asp3Phe1)n, (Asp2Phe1)n, (Asp1Phe1)n, (Asp1Phe2)n, and (Asp1Phe3)n, containing the hydrophilic amino acid, aspartic acid (Asp) and the hydrophobic amino acid, phenylalanine (Phe), were synthesized. Their behaviour in aqueous solution was investigated by performing fluorescence quenching and non-radiative energy transfer (NRET) experiments which were complemented by dynamic (DLS) and static (SLS) light scattering. The photophysical properties of the polypeptides were dependent on their Phe content. An increase in the Phe content led to an increase in the extinction coefficient, fluorescence quantum yield, and fluorescence average lifetime of the polypeptides. Circular dichroism experiments revealed that except for the (Asp1Phe3)n polypeptide, which adopts an alpha-helical conformation in aqueous solution, the other polypeptides did not adopt any known conformation in solution. The fluorescence quenching studies performed using molecular pyrene physically bound to the polypeptide via hydrophobic interactions resulted in protective quenching for the (Asp1Phe1)n, (Asp1Phe2)n, and (Asp1Phe3)n polypeptides, with some pyrenes having a lifetime of ~300 ns. Evidence for protective quenching was also observed in the polypeptides richer in Phe, when pyrene was covalently attached onto the polypeptides. However pyrene was found to be fully exposed to the quencher solution for the more hydrophilic polypeptides. The presence of NRET between a naphthalene labeled polypeptide and a pyrene labeled polypeptide for the (Asp1Phe2)n and (Asp1Phe3)n polypeptides and its absence for the (Asp3Phe1)n, (Asp2Phe1)n, and (Asp1Phe1)n polypeptides led to the conclusion that those polypeptides richer in Phe generate interpolymeric aggregates which provide protection to a hydrophobic cargo like molecular pyrene whereas the hydrophilic polypeptides exist predominantly as unimolecular micelles. These results were confirmed by DLS and SLS experiments.

In this paper, an improved method [1] for the chemical synthesis of 2SeU-RNA was reported using a streamlined strategy employs 2'-O-Thiomopholine-4-carbothioate protecting group. And single step deprotection of the resulting oligoribonucleotide product using 1,2-diamines/toluene under anhydrous conditions would retain the Selenium atom introduced on the 2-possiton of the modified Uracil. The process is doable with most standard heterobase protection and deprotection, it greatly simplifies the synthesis of 2SeU-RNAs and can be applied to other Selenium modified RNAs synthesis. It makes the synthesis of RNA become as simple and efficient as the chemical synthesis of DNA. Furthermore, the design and synthesis of self-assembling 2SeU-RNA square are reported which enable further structure studies and application of unique 2SeU-RNAs.

Preliminary work towards the development of novel biosensing interfaces for EMPAS (ElectroMagnetic Piezoelectric Acoustic Sensor) is presented in this manuscript. This method involves the use of unprecedented thiosulfonate-based linkers to construct robust and durable SAMs (Self-Assembling Monolayer) onto piezoelectric quartz crystals, which can chemoselectively immobilize thiol-containing biomolecules under aqueous conditions in a single, straightforward, reliable and coupling-free manner. Initial efforts are devoted to the construction of SAMs and the subsequent immobilization of thiol-containing biomolecules, and then characterization by CAMs (Contact Angle Measurement) and ARXPS (Angle-Resolved X-ray Photoelectron Spectroscopy). This method is then implemented into the construction of biosensing interfaces dedicated to the detection of avidin. With the incorporation of OEG (Oligo(Ethylene Glycol)) backbone and diluent in the method, 14-fold difference in signal response of EMPAS was observed between biotinylated and unfunctionalized SAMs.

Preliminary work towards the development of novel biosensing interfaces for EMPAS (ElectroMagnetic Piezoelectric Acoustic Sensor) is presented in this manuscript. This method involves the use of unprecedented thiosulfonate-based linkers to construct robust and durable SAMs (Self-Assembling Monolayer) onto piezoelectric quartz crystals, which can chemoselectively immobilize thiol-containing biomolecules under aqueous conditions in a single, straightforward, reliable and coupling-free manner. Initial efforts are devoted to the construction of SAMs and the subsequent immobilization of thiol-containing biomolecules, and then characterization by CAMs (Contact Angle Measurement) and ARXPS (Angle-Resolved X-ray Photoelectron Spectroscopy). This method is then implemented into the construction of biosensing interfaces dedicated to the detection of avidin. With the incorporation of OEG (Oligo(Ethylene Glycol)) backbone and diluent in the method, 14-fold difference in signal response of EMPAS was observed between biotinylated and unfunctionalized SAMs.

We used self-assembling tunnel junctions (SATJs) to study the electron transport through films of the molecular magnets, Mn12-Acetate. Pulse laser deposition (PLD) was used to deposit two monolayers of Mn12-Acetate on thin Pt wires (diameter 0.001 in). The electron tunneling current was measured with typical bias voltages from -1 to 1 V at liquid helium temperature, 4.2 K. I, dI/dV , and d2I/dV 2 signals were directly acquired with the aid of a current amplifier and two lock-in-amplifiers. Results show that the differential conductance is approximately 10â 6 S for bias voltages 0.04 V < or =| V |< or = V and exhibits a strong voltage dependence. In the region | V |< or = 0.04 V, we find a zero-bias feature (ZBF) in which the differential conductance is suppressed. In some samples, we observe I -V staircases which we attribute to electrons "hopping" between the electrodes and the molecules. The observed hysteresis was attributed to the slow relaxation of molecules re-orienting within the junction. Abrupt conductance jumps at a bias voltage of -0.12 V were also observed and may indicate state transitions in the Mn12-Acetate molecules. Furthermore, we observed that the zero bias feature (ZBF) can switch from an enhancement to a suppression of the differential conductance. A dip and dry (DAD) method was also used to form films of Mn12-Acetate on Al and Pt wires. Although the conductances were similar to those obtained using the PLD method, there were some subtle differences. In particular, we did not observe the I -V staircases and the state jumps were more ambiguous. The differential conductance for the Mn12-Acetate films on Al wires were typically 10- 7 S, which we attributed to the oxide layer on Al surfaces. We have also found substantial changes in the I - V characteristics when the Pt wires coated with the Mn12-Acetate films were stored in 10-2 Torr for 6 months. In particular, we observed many new features such as peaks in the conductance as a function as the bias voltage. We believe that these effects may be caused by the slow oxidation of the Mn12-Acetate molecules.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第17600号 / 工博第3759号 / 新制||工||1573(附属図書館) / 30366 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 松田 建児, 教授 秋吉 一成 / 学位規則第4条第1項該当

京都大学 / 新制・課程博士 / 博士(医学) / 甲第24495号 / 医博第4937号 / 新制||医||1063(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 生田 宏一, 教授 杉田 昌彦, 教授 鈴木 実 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Peptide amphiphiles (PAs), peptides that self-assemble into hydrogels with a nanofibrous network, are interesting biomaterials due to their biocompatibility and biodegradability. Self-assembling peptide-based materials include a wide range of peptide motifs that form one-dimensional nanostructures in aqueous solution. Two different PAs are considered in this M.S. thesis work: lipidated peptides, and gas-releasing peptides (GRPs). These biomaterials have been developed to function as potential therapeutics that promote the growth of new blood vessels. The analyses conducted on the lipidated peptides, which were designed to include a peptide sequence that promotes angiogenesis, include cytotoxicity, viability, and tube formation assays. The GRPs were designed to release H2S, which is also capable of promoting angiogenesis. Several characteristic properties of the GRPs were analyzed, including morphology, mechanics, self-assembly, and gas release rates. Furthermore, cytotoxicity assays were conducted followed by the demonstration of gas uptake in endothelial cells. / Master of Science

Statics, dynamics, rheology and scission-recombination kinetics of self-assembling linear micelles are investigated at equlibrium state and under shear flow by computer simulations using a newly proposed mesoscopic model. We model the micelles as linear sequences of Brownian beads whose space-time evolution is governed by Langevin dynamics. A Monte Carlo algorithm controls the opening of a bond or the chain-end fusion. A kinetic parameter omega modelling the effect of a potential barrier along a kinetic path, is introduced in our model. For equilibrium state we focus on the analysis of short and long time behaviors of the scission and recombination mechanisms. Our results show that at time scales larger than the life time of the average chain length, the kinetics is in agreement with the mean-field kinetics model of Cates. By studying macroscopic relaxation phenomena such as the average micelle length evolution after a T-jump, the monomer diffusion, and the zero shear relaxation function, we confirm that the effective kinetic constants found are indeed the relevant parameters when macroscopic relaxation is coupled to the kinetics of micelles. For the non-equilibrium situation, we study the coupled effects of the shear flow and the scission-recombination kinetics, on the structural and rheological properties of this micellar system. Our study is performed in semi-dilute and dynamically unentangled regime conditions. The explored parameter omega range is chosen in order for the life time of the average size chain to remain shorter than its intrinsic (Rouse) longest relaxation time. Central to our analysis is the concept of dynamical unit of size Lambda, the chain fragment for which the life time tau_Lambda and the Rouse time are equal. Shear thinning, chain gyration tensor anisotropy, chain orientation and bond stretching are found to depend upon the reduced shear rate Beta_Lambda=gamma dot*tau_Lambda while the average micelle size is found to decrease with increasing shear rate, independently of the height of the barrier of the scission-recombination process.