Base damage, local sequence context andTP53mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability

The mutational pattern for the TP53 tumour suppressor gene in lung tumours differs to other cancer types by having a higher frequency of G:C>T:A transversions. The aetiology of this differing mutation pattern is still unknown. Benzo[a]pyrene,diol epoxide (BPDE) is a potent cigarette smoke carcinogen that forms guanine adducts at TP53 CpG mutation hotspot sites including codons 157, 158, 245, 248 and 273. We performed molecular modelling of BPDE-adducted TP53 duplex sequences to determine the degree of local distortion caused by adducts which could influence the ability of nucleotide excision repair. We show that BPDE adducted codon 157 has greater structural distortion than other TP53 G:C>T:A hotspot sites and that sequence context more distal to adjacent bases must influence local distortion. Using TP53 trinucleotide mutation signatures for lung cancer in smokers and non-smokers we further show that codons 157 and 273 have the highest mutation probability in smokers. Combining this information with adduct structural data we predict that G:C>T:A mutations at codon 157 in lung tumours of smokers are predominantly caused by BPDE. Our results provide insight into how different DNA sequence contexts show variability in DNA distortion at mutagen adduct sites that could compromise DNA repair at well characterized cancer related mutation hotspots

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

<p>Abstract</p> <p>Background</p> <p>An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations.</p> <p>Results</p> <p>Most of the dinucleotide steps in free DNA display high flexibility, assuming different conformations in a sequence-dependent fashion. With the exception of the AA/TT and GA/TC steps, which are 'A-phobic', and the GG/CC step, which is 'A-philic', the dinucleotide steps show no preference for A or B forms of DNA. Protein-bound DNA adopts the B-conformation most often. However, in certain cases, protein-binding causes the DNA backbone to take up energetically unfavourable conformations. At the gross structural level, several protein-bound DNA duplexes are observed to assume a curved conformation in the absence of any large distortions, indicating that a series of normal structural parameters at the dinucleotide and trinucleotide level, similar to the ones in free B-DNA, can give rise to curvature at the overall level.</p> <p>Conclusion</p> <p>The results illustrate that the free DNA molecule, even in the crystalline state, samples a large amount of conformational space, encompassing both the A and the B-forms, in the absence of any large ligands. A-form as well as some non-A, non-B, distorted geometries are observed for a small number of dinucleotide steps in DNA structures bound to the proteins belonging to a few specific families. However, for most of the bound DNA structures, across a wide variety of protein families, the average step parameters for various dinucleotide sequences as well as backbone torsion angles are observed to be quite close to the free 'B-like' DNA oligomer values, highlighting the flexibility and biological significance of this structural form.</p

Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence

BACKGROUND: Local sequence context is known to have an impact on the mutational pattern seen in cancer. The RAS genes and a smoking carcinogen, Benzo[a]pyrene diol epoxide (BPDE), have been utilised to explore these context effects. BPDE is known to form an adduct at the guanines in a number of RAS gene sites, KRAS codons 12, 13 and 14, NRAS codon 12, and HRAS codons 12 and 14. RESULTS: Molecular modelling techniques, along with multivariate analysis, have been utilised to determine the sequence influenced differences between BPDE-adducted RAS gene sequences as well as the local distortion caused by the adducts. CONCLUSIONS: We conclude that G:C > T:A mutations at KRAS codon 12 in the tumours of lung cancer patients (who smoke), proposed to be predominantly caused by BPDE, are due to the effect of the interaction methyl group at the C5 position of the thymine base in the KRAS sequence with the BPDE carcinogen investigated causing increased distortion. We further suggest methylated cytosine would have a similar effect, showing the importance of methylation in cancer development. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13065-021-00777-8

Probabilistic grammatical model of protein language and its application to helix-helix contact site classification

BACKGROUND: Hidden Markov Models power many state‐of‐the‐art tools in the field of protein bioinformatics. While excelling in their tasks, these methods of protein analysis do not convey directly information on medium‐ and long‐range residue‐residue interactions. This requires an expressive power of at least context‐free grammars. However, application of more powerful grammar formalisms to protein analysis has been surprisingly limited. RESULTS: In this work, we present a probabilistic grammatical framework for problem‐specific protein languages and apply it to classification of transmembrane helix‐helix pairs configurations. The core of the model consists of a probabilistic context‐free grammar, automatically inferred by a genetic algorithm from only a generic set of expert‐based rules and positive training samples. The model was applied to produce sequence based descriptors of four classes of transmembrane helix‐helix contact site configurations. The highest performance of the classifiers reached AUCROC of 0.70. The analysis of grammar parse trees revealed the ability of representing structural features of helix‐helix contact sites. CONCLUSIONS: We demonstrated that our probabilistic context‐free framework for analysis of protein sequences outperforms the state of the art in the task of helix‐helix contact site classification. However, this is achieved without necessarily requiring modeling long range dependencies between interacting residues. A significant feature of our approach is that grammar rules and parse trees are human‐readable. Thus they could provide biologically meaningful information for molecular biologists

Role of intermediate filament desmin in development of desmin-related myopathy

Desmin is a major intermediate filament of muscle cells, serving to transmit mechanical forces and propagate mechanochemical signals, to coordinate contraction and relaxation cycles, and to stabilize the positioning of cellular organelles, e.g. mitochondria. Around 70 desmin gene mutations have been reported in conjunction with desmin-related myopathy. Desmin-related myopathy can be described as pathophysiological complex, accompanied by desmin intracellular aggregate accumulation and impairment of desmin interactions with structural proteins, signal molecules, and cell organelles. However, the precise molecular mechanism underlying desmin-related myopathy have not been described yet. There are speculations if it is connected with toxic effects of desmin aggregates or with violation of desmin mechanotransduction functions. The general aim of the present PhD project was to extend existing knowledge about the molecular machinery on how desmin gene mutations lead to the development of desmin-related myopathy, with an emphasis on development of cardiomyopathies. To address this aim the following research questions were stated: (i) genetic study of a group of patients with cardiomyopathies in order to describe novel mutations in the desmin gene, and to assess the frequency of DES A213V; (ii) genetic study by means of next-generation sequencing approach of a group of patients with idiopathic restrictive cardiomyopathy in order to describe novel genetic variants associated with disease; (iii) functional study of desmin gene point mutations effect on mitochondrial properties. The main findings regarding genetic background were: (i) DES A213V represents a disease-modifying polymorphism, rather than disease-related mutation, since it was found both in patients and healthy donors; (ii) combination of disease-related– disease-modifying or disease-related–disease-related genetic variants, rather than single disease-related mutation, determined the development of idiopathic restrictive cardiomyopathy. Most proteins of these combinations belonged to four functional groups: sarcomeric contractile proteins, mechanosensing Z-disc proteins, nuclear membrane, and outer mitochondrial membrane proteins. Functional studies of the impact of desmin mutations on mitochondria showed that aggregate-prone mutations decreased mitochondrial calcium uptake, as well as depressed maximal oxygen consumption rate and spare respiratory capacity. In contrast, non-aggregate-prone mutations did not disturb mitochondrial calcium. They did, however, result in the reduction of maximal oxygen consumption rate and affected spare respiratory capacity. To conclude, (i) distortion of desmin mechanotransduction functions plays an important role in desmin-related myopathy onset, affecting mitochondrial properties; (ii) combination of mutations in genes encoding sarcomeric contractile and mechanosensing proteins, rather than a single mutation, predisposes to the development of cardiomyopathy. These data facilitate understanding of molecular pathways underlying desmin-related myopathy development, and increase existing knowledge of intracellular interactions within the muscle cell

pi-Turns: types, systematics and the context of their occurrence in protein structures

<p>Abstract</p> <p>Background</p> <p>For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures.</p> <p>Results</p> <p>An analysis of protein structures indicates that at least 20% of π-turns occur independent of the Schellman motif. The two categories of π-turns, designated as π-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length β- and α-turns, π-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C^α-atoms, and this resulted in a comparable number of non-hydrogen-bonded π-turns (π-NHB). The presence of shorter β- and α-turns within all categories of π-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied.</p> <p>Conclusion</p> <p>π-turns have been characterized, first using hydrogen bond and the distance between C^αatoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the π-HB turns, being located on surface cavities, have functional role and there is also sequence conservation.</p

카이랄 나노구조의 플라즈몬 커플링을 기반한 원편광 이색성 변조

학위논문(박사) -- 서울대학교대학원 : 공과대학 재료공학부, 2022.2. 남기태.카이랄 메타 물질은 뛰어난 광 물질 상호 작용으로 인하여 나노 광자 분야에서 큰 관심을 받아왔다. 다년간의 연구를 통하여 최첨단 리소그래피 기술과 분자 조립 스캐폴드를 사용하여 카이랄 나노구조가 제작되어 왔다. 기하학적 비대칭성을 지니는 카이랄 무기 금속 나노 물질은 대칭성을 가지는 나노 물질에서 얻을 수 없었던 독특한 물리적 현상을 나타낼 수 있다. 카이랄 나노 구조는 음의 굴절률, 분자 감지 및 광대역 원형 편광과 같은 광학적 효과를 나타내기 위해 사용될 수 있다. 이러한 카이랄 메타 물질의 뛰어난 광학 특성을 실제 장치에 통합하기 위해서는 섬세하게 설계된 광학적 성질을 가지는 카이랄 구조를 달성하는 것이 필요하다. 그러나 고가의 제조비용 및 설비, 복잡한 제조 과정 및 제한된 해상도로 인해 카이랄 메타 물질을 실제 장치로 통합하는 데 제한이 있어왔다. 이러한 한계를 극복하기 위해서는 카이랄 나노 구조 제어를 위한 유연한 방법론을 개발하는 것이 요구된다. 본 학위 연구 에서는 펩타이드를 이용한 나노 입자 형태의 다양화와 나노 구조에서의 플라즈몬 커플링을 이용한 광학적 반응의 추가적인 조절이 앞서 언급한 한계를 해결하기 위한 유망한 대안이 될 수 있음을 제안한다. 본 학위 논문은 카이랄 나노 구조의 발달에 대한 이해와 조절을 통해 플라즈몬 커플링을 이용하여 카이랄 광학 응답을 조절할 수 있는 플랫폼을 제시한다. 생체분자를 이용한 플라즈몬 나노 입자의 콜로이드 합성에 대한 최근 연구결과는 합성 과정에 관여하는 카이랄성 인코더인 분자를 변경함으로써 새로운 형태와 광학적 특성을 가진 나노입자를 합성할 수 있음을 시사한다. 또한 단일 플라즈몬 입자의 광학 응답은 플라즈몬 커플링을 사용하여 증폭되고 민감하게 변조될 수 있다. 여러 플라즈몬 나노 입자가 인접할 경우, 입자 공명의 혼성화가 유도되어 공명을 크게 변화시킨다. 플라즈몬 나노 구조의 형태와 카이랄성을 제어하기 위한 새로운 전략을 수립하기 위하여, 우리는 먼저 생체분자에 의해 유도되는 무기 카이랄성에 초점을 맞추었다. 무기 표면에서의 원자 왜곡 또는 거시적 재구성을 통한 카이랄성의 진화에 대한 기존 연구는 카이랄 나노 구조 제어를 위한 새로운 전략 수립에 중요한 통찰력을 제공한다. 본 학위논문에서는 카이랄 광학 반응의 이해와 조절을 단일 나노 입자와 시스템적 제어의 두 가지 관점에서 소개한다. 나노 재료 공학의 발전으로 나노 규모에서 정확한 형태학적 제어가 가능한 콜로이드 합성 방법이 개발되었다. 다양한 할로겐화물 이온, 금속 이온 및 유기 분자를 흡착제로 사용하면 특정 Miller 지수로 결정면을 부동태화하여 결정면과 나노입자 형태를 손쉽게 제어할 수 있다. 또한 종자 매개 방법은 높은 Miller-index 결정면을 높은 균일도로 생성할 수 있으므로 나노 입자의 형태를 제어하는 중요한 전략으로 사용된다. 우리는 합성에 첨가하는 유기 분자를 변경하여 금 나노 입자의 성장 및 카이랄성 진화에 대한 광범위한 이해를 제공한다. 이를 위하여 γ-글루타밀시스테인(γ-Glu-Cys) 및 시스테이닐글리신(Cys-Gly) 을 사용하여 합성된 금 나노 입자의 성장 경로와 키랄성 진화가 결정학적 관점에서 분석되었다. γ-Glu-Cys을 이용하여 합성된 금 나노 입자의 경우 돌출된 카이랄 날개를 가지는 정육면체 구조로 발달한다. 반면에, Cys-Gly을 이용하여 합성된 나노입자의 경우 타원형의 공동 구조를 가진 마름모꼴 12면체로 발달하며, 이로 인해 두 나노 입자는 서로 다른 카이랄 광학 반응을 보인다. 시간에 따른 나노 입자의 성장 분석을 통해 γ-Glu-Cys와 Cys-Gly가 서로 다른 중간 형태를 지니며 생성한다는 것을 알 수 있었다. γ-Glu-Cys는 오목한 육팔면체 모양의 중간체를 유도하는 반면 Cys-Gly는 오목한 마름모꼴 십이면체의 중간체를 보인다. 이러한 결과는 펩타이드와 금 표면 간의 상호 작용을 이해함으로써 카이랄 구조와 그에 따른 광학 반응을 조절할 수 있음을 시사한다. 생체 분자를 이용한 카이랄 나노구조의 합성은 주로 플라즈몬 물질에서 연구되어 왔지만, 촉매 활성을 지녀 카이랄 촉매로 사용될 수 있는 카이랄 금속 산화물을 합성하려는 시도 또한 카이랄 물질의 응용 확대를 위한 새로운 방향으로 제시되고 있다. 생체 분자를 이용한 카이랄 금속 산화물 합성에서의 기존 연구는 단일 아미노산에 국한되어 있지만, 카이랄성 발달을 이해하고 확장 가능한 합성 전략을 수립하기 위해서는 펩타이드로의 서열 확장이 요구된다. 본 연구에서는 Tyr-Tyr-Cys 펩타이드를 서열확장을 위한 리간드로 선택하여, 코발트 산화물에서 펩타이드를 이용한 카이랄성 발현을 탐구하였다. 펩타이드 리간드를 이용하여 합성된 카이랄 코발트 산화물 나노 입자는 자외선 및 가시광선 영역에서 0.01의 뛰어난 비대칭 인자를 나타냈다. 또한, 2D NMR 분광 분석을 통해 나노 입자 표면의 펩타이드 리간드의 3차원 입체구조를 규명하였다. 또한 펩타이드 리간드의 시퀀스에 따른 카이랄 코발트 산화물 나노 입자의 발달을 분석하여 Tyr-Tyr-Cys 리간드의 싸이올 그룹과 카복실 그룹이 카이랄성 발달에 중요한 역할을 담당함을 규명하였다. 본 연구 결과는 무기 결정에 카이랄성을 발현하는 펩타이드의 역할이 상호 작용하는 물질에 따라 달라질 수 있으며, 카이랄 광학 특성의 변화를 야기할 수 있음을 시사한다. 단일 플라즈몬 나노 입자의 광학 신호는 플라즈몬 커플링을 통하여 증폭되고 민감하게 제어될 수 있다. 여러 개의 플라즈몬 나노 입자가 인접할 경우, 입자 공명의 혼성화가 일어나 공명을 크게 변화시킨다. 이러한 맥락에서, 본 연구에서는 플라즈몬 커플링을 카이랄 플라즈몬 나노 입자에 적용하여 카이랄 광학 특성을 제어하고자 하였다. 이를 위하여 카이랄 금 나노 입자를 기판에 코팅하고 나노 크기의 플라즈몬 금속 층을 증착하여 메타 물질을 제작하였다. 플라즈몬 결합으로 인한 광학 특성의 변화는 투과 기반 및 확산 반사 기반 원편광 이색성 (cirular dichroism, CD) 분광법을 통해 분석되었다. 카이랄 금속 나노 입자 기반 메타 물질의 광학적 분석을 통해 CD 스펙트럼의 피크 위치, 세기 및 부호가 플라즈몬 커플링에 의해 변화함을 알 수 있었다. 또한, 플라즈몬 커플링에 의해 생성된 모드는 나노구조체의 크기, 거리 및 주변 굴절률에 따라 크게 변화하였다. 더 나아가, 카이랄 금 나노 입자에 실리카 쉘의 플라즈몬 나노입자의 광학 특성 및 안정성의 제어가 가능함을 규명하였다. 본 학위 연구에서는 나노 입자의 카이랄성 발달에 펩타이드 리간드가 미치는 역할을 이해함으로써 단일 나노 입자 수준에서 CD 신호의 제어를 달성하였다. 또한 플라즈몬 커플링을 사용하여 카이랄 나노 구조의 광학적 특성을 조절하는 방법론이 확립되었다. 본 연구를 통하여 개발된 카이랄 나노 구조에서 광학 특성의 조절을 위한 방법론은 카이랄 메타 물질을 실용적인 광학 장치로 통합하는 것을 용이하게 할 것으로 기대된다.Chiral metamaterials have been actively pursued in the field of nanophotonics due to their exceptional light-matter interactions. For decades, numerous attempts have been conducted to fabricate chiral nanostructure using state-of-the-art lithography techniques and molecular-assembly scaffolds. Possessing this geometric property, inorganic metal nanomaterials could exhibit fascinating physical phenomena which was difficult to be achieved in symmetric nanomaterials. Chiral nanostructures have greatly expanded the design to demonstrate chiroptic effects such as a negative refractive index, sensitive chiral sensing, and broad-band circular polarizer. In order to integrate the fascinating properties of chiral metamaterials into practical devices, it is necessary to achieve precisely defined chiral morphologies and chiroptic properties. However, the requirement for expensive facilities, the complexity of the process, and the limited resolution had restricted the translation of chiral metamaterials into real devices. Therefore, developing flexible methodologies for nanostructure control is important to address these limitations and provide new directions. Through this study, we propose that the diversification of nanoparticle morphology using peptide molecules and further modulation of the optical response utilizing plasmonic coupling of nanostructures can be a promising alternative to solve the above-mentioned limitations. In this thesis, we present a platform that can modulate the chiroptic response using plasmon coupling through understanding and regulation of the development of chiral nanostructures. Recent study on the colloidal synthesis of plasmonic nanoparticles using biomolecules suggests that nanoparticles with novel morphology and optical property can be achieved by altering molecules, which are chirality encoders, involved during the synthesis. In addition, the optical response of a single plasmonic particle can be amplified and sensitively modulated using plasmon coupling. When several nanoscale plasmonic particles are adjacent to each other, hybridization of particle resonance is induced, which significantly changes the resonance. To establish new strategies for controlling the morphology and chirality of plasmonic nanostructures, we have first studied previous studies on bio-inspired pathways for complex nanostructures, focusing on the inorganic chirality induced by biomolecules in Chapter 2. Importantly, the interactions at the interface between biomolecules and inorganic surfaces provide an important insight into the evolution of chirality through atomic distortion or macroscopic reconstruction. Chapter 3 describes the experimental procedures, and Chapter 4, 5, and 6 describe the understanding and modulation of the chiroptic response from the two perspectives of single nanoparticles and systemic control. Advances in nanomaterial engineering have enabled the development of colloidal synthesis methods for precise morphological control at the nanoscale. The use of various halide ions, metal ions and organic molecules as adsorbates can control the crystal facet and nanoparticle morphology by passivating the crystal facet with a specific Miller index. In addition, the seed-mediated method can synthesize high-Miller-index crystal facets with high uniformity, and thus is being used as an important strategy for controlling NP morphology. In this thesis, we have provided a broad understanding of the growth and chirality evolution in gold NPs by adjusting the type of additive molecules. We have analyzed the growth pathway and chirality evolution of the γ-glutamylcysteine- (γ-Glu-Cys-) and cysteinylglycine- (Cys-Gly-) directed gold NPs from a crystallographic perspective. Gold NPs developed into a cube-like structure with protruding chiral wings in the presence of γ-Glu-Cys, whereas the NPs synthesized with Cys-Gly exhibited a rhombic dodecahedron-like outline with elliptical cavity structures, showing different chiroptic responses. Through time-dependent analysis, we reported that γ-Glu-Cys and Cys-Gly generate different intermediate morphologies. γ-Glu-Cys induced concave hexoctahedra-shaped intermediate, whereas Cys-Gly showed concave rhombic dodecahedra-shaped intermediate. These results showed that the chiral structure and resulting chiroptic response can be modulated through understanding the interaction between peptides and gold surfaces. Molecule-directed synthesis of chiral nanostructure has been mainly studied in plasmonic materials, but attempts to synthesize chiral metal oxides that can be used as chiral catalysts due to their catalytic activity has been suggested as a new direction for expanding the application of chiral materials. Existing studies on the synthesis of chiral metal oxide using molecule have been limited to single amino acids, but sequence expansion with peptides is required to understand the chirality evolution and achieve a scalable synthetic strategy. In this thesis, Tyr-Tyr-Cys tripeptide including tyrosine and cysteine were selected as peptide ligands and the role of peptide in developing chirality in cobalt oxide was explored. Synthesized chiral cobalt oxide nanoparticles showed a g-factor of 0.01 in the UV–visible region. In addition, the 3D conformation of the peptide ligand on the nanoparticle surfaces was identified by 2D NMR spectroscopy analysis. Furthermore, the sequence effect of Tyr-Tyr-Cys developing chiral cobalt oxide was analyzed, demonstrating that the thiol group and carboxyl group of the Tyr-Tyr-Cys ligand played an important role in chirality evolution. This results suggest that the role of the peptides can vary depending on the interacting material, leading to further variability in chiroptical properties. The optical signal of a single plasmonic particle can be amplified and sensitively controlled using plasmon coupling. When several nanoscale plasmonic particles are adjacent to each other, hybridization of particle resonance occurs, which significantly changes the resonance. In this context, plasmonic coupling which has been mainly studied in achiral plasmon structures, was applied to chiral plasmonic nanoparticles to control chiroptical properties. In this thesis, we demonstrated the fabrication of metamaterial by coating chiral gold nanoparticles on a substrate and depositing a nanoscale plasmonic metal layer. In order to investigate changes in optical properties due to plasmon coupling, transmission-based and diffuse reflectance circular dichroism (CD) spectroscopy were utilized. Through this, it was confirmed that the resonance position, magnitude, and sign of the CD spectrum were changed by plasmon coupling. In addition, the coupled plasmon mode was significantly changed according to the dimension, distance, and refractive index of the nanostructure. Furthermore, synthesis of chiral gold-silica core-shell NPs enables versatile control of the structure and properties of plasmonic nanoparticles, facilitating their application to tailored plasmon coupling. In conclusion, by understanding the role of peptides in nanoparticle development, CD manipulation has been achieved at the single nanoparticle level. In addition, a methodology for modulating the optical properties of chiral nanostructures using plasmon coupling has been established. We believe the development of versatile methodology for modulation of the chiroptical response in chiral nanostructures ultimately facilitate integration of the chiral metamaterials into practical optical devices.Chapter 1. Introduction 1 1.1 Chirality in Nature 1 1.2 Chiral Plasmonic Nanostructure 9 1.3 Objective of Thesis 21 Chapter 2. Fabrication of Chiral Inorganic Nanostructure and Its Optical Properties 24 2.1 Fabrication of Chiral Nanostructures using Hard Approach 24 2.2 Biomolecule-Directed Chiral Nanostructure 29 2.2.1 Biomolecule-Conjugated Inorganic Nanoparticles 29 2.2.2 Chirality Development by Biomolecule-Induced Local Distortion 36 2.2.3 Biomolecule-Directed Chiral Morphology 44 Chapter 3. Experimental Procedures 62 3.1 Synthesis of Chiral Gold Nanoparticles 62 3.2 Synthesis of Chiral Cobalt Oxide Nanoparticles 64 3.3 Synthesis of Chiral Gold-Silica Core-Shell Nanoparticles 66 3.4 Optical Characterization of Chiral Nanostructures 67 Chapter 4. Dipeptide-Directed Chiral Gold Nanoparticles 69 4.1 Introduction 69 4.2 Solution-Based Synthesis of Dipeptide-Directed Chiral NPs 72 4.3 Morphology Analysis of γ-Glu-Cys- and Cys-Gly-directed NPs 79 4.4 Time-Dependent Analysis of Chiral Morphology Development 83 4.5 Concentration-Dependent Chiral Morphology and Chiroptical Responses 91 4.6 Sequence Effects 101 4.7 Conclusion 102 Chapter 5. Peptide-Directed Chiral Cobalt Oxide Nanoparticle 103 5.1 Introduction 103 5.2 Synthesis of Chiral Cobalt Oxide Nanoparticles using Tyr-Tyr-Cys 107 5.3 Effect of Synthetic Parameters on Chirality Development of Chiral Cobalt Oxide Nanoparticles 114 5.4 3D Conformation of Tyr-Tyr-Cys Ligand 120 5.5 Sequence Effect of the Tyr-Tyr-Cys 125 5.6 Magnetic Circular Dichroism in Chiral Cobalt Oxide Nanoparticles. 129 5.7 Conclusion 134 Chapter 6. Circular Dichroism Manipulation based on Plasmonic Coupling of Chiral Nanostructures 136 6.1 Introduction 136 6.2 Chiroptical Property of Helicoid-Based Plasmonic Nanostructure 138 6.3 Effect of Chiral Gap Structure 145 6.4 Spectral Manipulation through Structural Parameter Control 149 6.5 Synthesis of Chiral Gold-Silica Core-Shell Nanoparticles 151 6.6 Conclusion 154 Chapter 7. Concluding Remarks 155 References 159박

Foldamers in Medicinal Chemistry

International audienc

Development and Application of a Synthetic Near Infrared Fluorescent Probe for Imaging Modulatory Neurotransmitters

Dopamine neurotransmission plays critical roles in brain function in both health anddisease and aberrations in dopamine neurotransmission are implicated in severalpsychiatric and neurological disorders, including schizophrenia, depression, anxiety, andParkinson’s disease. Until recently, measuring the dynamics of dopamine and otherneurotransmitters of this class could not be achieved at spatiotemporal resolutionsnecessary to study how dopamine regulates the plasticity and function of neurons and neuralcircuits, and how dysfunctions in this regulation lead to disease. Probes that satisfy criticalattributes in spatiotemporal resolution and chemical selectivity are needed to facilitateinvestigations of dopamine neurochemistry.To address this need, this dissertation describes the synthesis and implementation ofan ultrasensitive near-infrared “turn-on” nanosensor (nIRCat) for the catecholamineneuromodulators dopamine and norepinephrine. To guide probe development, we presentresults from a computational model that offers insight into the spatiotemporal dynamics ofdopamine in the striatum, a subcortical structure that is enriched in dopamine. With thismodel, we elucidated the kinetic requirements for a prototypical optical indicator as well asoptimal imaging frame rates needed for measuring dopamine neurochemical dynamics.Stochastic modeling of dopamine dynamics, driven by kinetic phenomena of vesicularrelease, diffusion and clearance, provide a platform to evaluate dopaminergic volumetransmission arising from a single terminal or ensemble terminal activity. With this work,we illustrate that only probes with kinetic parameters in a particular range are feasible fordopamine imaging at spatiotemporal scales likely to be encountered in brain tissue.In two subsequent chapters, we describe the development and in vitrocharacterization of nIRCats, synthesized from functionalized single wall carbon nanotubes(SWCNT) that fluoresce in the near infrared range of the spectrum. We show that nIRCatsexhibit maximal relative change in fluorescence intensity (ΔF/F0) of up to 35-fold inresponse to catecholamines and have optimal dynamic range that span physiologicalconcentrations of their target brain analytes. Through a combination of experimental andmolecular dynamics approaches, we elucidate the photophysical principles and intermolecularinteractions that govern the molecular recognition and fluorescence modulation of nIRCats by dopamine.Finally, we demonstrate that nIRCat can be used to measure electrically andoptogenetically evoked release of dopamine in striatal brain slices, revealing hotspots ofactivity with a median size of 2 μm, and exhibiting a log-normal size distribution that extendsup to 10 μm. Moreover, nIRCats are shown to be compatible with dopamine pharmacologyand permit studies of how receptor-targeting drugs modulate evoked dopamine release. Ourresults suggest nIRCats may uniquely support similar explorations of processes that regulatedopamine neuromodulation at the level of individual synapses, and exploration of the effectsof receptor agonists and antagonists that are commonly used as psychiatric drugs andpsychoactive molecules that modulate the release and clearance profiles of dopamine. Weconclude that nIRCats and other nanosensors of this class can serve as versatile syntheticoptical tools to monitor interneuronal chemical signaling in the brain extracellular space atspatial and temporal scales pertinent to the encoded information