Artificial Molecular Systems for Complex Functions Based on DNA Nanotechnology and Cell‐Sized Lipid Vesicles

Cells are highly functional and complex molecular systems. Artificially creating such systems remains a challenge, which has been extensively studied in various research fields, including synthetic biology and molecular robotics. DNA nanotechnology is a powerful tool for bottom-up engineering for constructing functional nanostructures or chemical reaction networks which can be utilized as components for artificial molecular systems. Encapsulation of these components into a giant unilamellar vesicle (GUV) composed of a lipid bilayer, the base structure of the cellular membrane, results in a functional cell-sized structure that partially mimics some cellular functions. This review discusses the studies contributing to the construction of GUV-based artificial molecular systems based on DNA nanotechnology. Molecular transport and signal transduction through lipid membranes are essential to uptake molecules from the environment and respond to stimuli. Membrane shaping relates to various functions, including motility and signaling. A chemical reaction network is required to autonomously regulate the system's functions. This review describes the functions realized using DNA nanostructures and DNA reaction networks. Given the designability and programmability of DNA nanotechnology, it may be possible that the functionality of artificial molecular systems could be comparable to or even surpass that of natural molecular systems.journal articl

Oligolysine Enhances and Inhibits DNA Condensate Formation

The formation of biomolecular condensates via phase separation relates to various cellular functions. Reconstituting these condensates with designed molecules facilitates the exploration of their mechanisms and potential applications. Sequence-designed DNA nanostructures enable the investigation of how structural design influences condensate formation and the construction of functional artificial condensates. Despite the high designability of DNA-based condensates, free nanostructures that do not assemble into condensates remain a challenge. Combining DNA nanostructures with other molecules, such as peptides, represents a promising approach to overcoming the limitations of DNA condensates and gaining a deeper understanding of molecular condensates. Herein, we report the effects of cationic oligolysines with several residues on DNA condensate formation assembled from Y-shaped DNA nanostructures. DNA condensate formation was enhanced by oligolysines at an appropriate L/P ratio, which refers to the ratio of positively charged amine groups in lysine (L) to negatively charged nucleic acid phosphate groups (P). Oligolysines with five residues enhanced condensate formation while maintaining the sequence-specific interaction of DNA. In contrast, oligolysines inhibited condensate formation depending on the L/P ratio and residue number. This was attributed to nanostructure deformation caused by oligolysines. These results suggest that the amount and length of cationic peptides significantly affect the self-assembly of branched DNA nanostructures. This study offers important insights into biomolecular condensates that can guide further development of DNA/peptide hybrid condensates to enhance the functions of artificial condensates for use in artificial cells and molecular robots.journal articl

Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller

In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the programmability of DNA are regarded as promising components for these systems. However, current systems rely on the manual addition of external stimuli, limiting the potential for autonomous molecular systems. Here, we show that DNA-based cascade reactions can act as a molecular controller that drives the autonomous assembly and disassembly of DNA-functionalized microtubules propelled by kinesins. The DNA controller is designed to produce two different DNA strands that program the interaction between the microtubules. The gliding microtubules integrated with the controller autonomously assemble to bundle-like structures and disassemble into discrete filaments without external stimuli, which is observable by fluorescence microscopy. We believe this approach to be a starting point toward more autonomous behavior of motor protein–based multicomponent systems with robotic functionalities.journal articl

Wireframe DNA Origami Capable of Vertex-protruding Transformation

Regulating dynamic behavior of the designed molecular structures provides a foundation for the construction of functional molecular devices. DNA nanotechnology allows conformational changes in two-dimensional and three-dimensional DNA origami nanostructures by introducing flexibility between the faces of the structures. However, dynamic transformations in wireframe DNA origami, composed solely of vertices and edges, remain challenging due to vertex-specific flexibility. We report a wireframe DNA origami capable of vertex-protruding transformation between the open- and closed-form with eight protruding vertices. This reversible transformation is driven by DNA hybridization and a toehold-mediated strand displacement reaction. Spacer strands between vertices and edges were designed to introduce flexibility. Coarse-grained molecular dynamics simulations demonstrated that a longer spacer increases conformational flexibility and can achieve the narrow angles required for the vertex-protruding transformation. The experimental results showed the successful assembly of the open-form structure under optimized salt conditions, as visualized through transmission electron microscopy images. Furthermore, the transformation between the open- and closed-form structures was demonstrated by the sequential addition of signal strands. This vertex-protruding transformation mechanism will expand the design approach of dynamic DNA nanostructures and help develop functional molecular devices for artificial molecular systems.journal articl

A case of rapidly progressive Salmonella aortic aneurysm with acute pericarditis manifesting as a precursor

We report a case of Salmonella cardiovascular infection presenting with acute pericarditis as a precursor to the rapid progression of aortic aneurysm. An 81-year-old man presented with persistent fever and chest pain worsened with inspiration and was admitted to a nearby hospital with a diagnosis of bacterial pericarditis. However, hoarseness emerged two days later, and the patient was transferred to our hospital because of concerns about extracardiac inflammatory foci. Computed tomography (CT) revealed a periaortic exudate and aortic arch aneurysm. After transfer, blood cultures confirmed Salmonella infection. Ampicillin (ABPC) was initiated for long-term treatment of Salmonella infection, and pericarditis was treated with ibuprofen and colchicine for approximately one month. The associated symptoms and inflammatory blood data significantly improved, but five weeks later, follow-up CT revealed enlargement of the arch aneurysm. Due to the patient's age and nutritional status, thoracic endovascular aortic repair (TEVAR) was performed along with continued ABPC. Postoperatively, the infection was well-controlled, and follow-up CT revealed a size reduction in the treated aneurysm. No recurrent Salmonella-related vascular events were observed for two years after TEVAR

A case of rapidly progressive Salmonella aortic aneurysm with acute pericarditis manifesting as a precursor

We report a case of Salmonella cardiovascular infection presenting with acute pericarditis as a precursor to the rapid progression of aortic aneurysm. An 81-year-old man presented with persistent fever and chest pain worsened with inspiration and was admitted to a nearby hospital with a diagnosis of bacterial pericarditis. However, hoarseness emerged two days later, and the patient was transferred to our hospital because of concerns about extracardiac inflammatory foci. Computed tomography (CT) revealed a periaortic exudate and aortic arch aneurysm. After transfer, blood cultures confirmed Salmonella infection. Ampicillin (ABPC) was initiated for long-term treatment of Salmonella infection, and pericarditis was treated with ibuprofen and colchicine for approximately one month. The associated symptoms and inflammatory blood data significantly improved, but five weeks later, follow-up CT revealed enlargement of the arch aneurysm. Due to the patient's age and nutritional status, thoracic endovascular aortic repair (TEVAR) was performed along with continued ABPC. Postoperatively, the infection was well-controlled, and follow-up CT revealed a size reduction in the treated aneurysm. No recurrent Salmonella-related vascular events were observed for two years after TEVAR

Nitroglycerin use and adverse clinical outcomes in elderly patients with acute coronary syndrome

Objective The primary care for acute coronary syndrome (ACS) includes the administration of nitroglycerin (GTN). This study aimed to investigate the association between the use of GTN before percutaneous coronary intervention (PCI) for ACS and clinical outcomes. Methods Nine-hundred and forty-seven patients who underwent PCI for ACS were examined and classified into two groups: those who were treated with GTN before PCI (GTN group) and those who were not (non-GTN group). The incidence of major adverse cardiovascular events (MACE), which consist of all-cause mortality, non-fatal myocardial infarction, stroke and rehospitalisation for heart failure at 1 year, was compared between the two groups. Results This study identified 289 patients with ACS who used GTN preceding PCI. Pre-PCI systolic blood pressure was significantly lower in the GTN group than in the non-GTN group (median (IQR); 132.0 (110.0–143.5) mm Hg vs 134.0 (112.0–157.0) mm Hg, respectively, p=0.03). Multivariate Cox regression analysis indicated that GTN use preceding PCI showed an independent association with the incidence of MACE (HR 1.57; 95% CI 1.09–2.28; p=0.016). Overall, the incidence of MACE 1 year after PCI for ACS was significantly higher in the GTN group than in the non-GTN group (log-rank test, p=0.024); however, this trend was consistently found in elderly patients aged ≥75 years (p=0.002) but not in non-elderly patients aged <75 years (p=0.773). Conclusions GTN use preceding PCI for ACS is associated with lower blood pressure and adverse clinical outcomes in elderly patients.Citation: Soichi Komaki, Yunosuke Matsuura, Hiroki Tanaka, Kohei Moribayashi, Yoshimasa Yamamura, Kazumasa Kurogi, Takeshi Ideguchi, Nobuyasu Yamamoto, Michikazu Nakai, Toshihiro Tsuruda, Koichi Kaikita, Nitroglycerin use and adverse clinical outcomes in elderly patients with acute coronary syndrome. Open Heart. 2024-01, 11(1), e002494, https://doi.org/10.1136/openhrt-2023-00249

Basal inferoseptal segment is highly susceptible to deformation in the clinical spectrum of transthyretin-derived amyloid cardiomyopathy

AIMS While the prevalence of transthyretin-derived amyloid cardiomyopathy (ATTR-CM) is on the rise, detailed understanding of its morphological and functional characteristics within the left ventricle (LV) across heart failure (HF) remains limited. METHODS AND RESULTS Utilizing two-dimensional (2D) speckle-tracking echocardiography, we assessed longitudinal strain (LS) in 63 histology-confirmed ATTR-CM patients. Additionally, cardiac magnetic resonance (CMR) images measured native T1 and extracellular volume (ECV), compared with LS across 18 LV segments. Patients were categorized into three groups based on HF status: Group 1 (no HF symptoms), Group 2 (HF with preserved LV ejection fraction), and Group 3 (HF with reduced LV ejection fraction). LS analysis unveiled susceptibility to deformation in the basal inferoseptal segment, persisting even in asymptomatic cases. CMR demonstrated increasing native T1 deviation, particularly evident in segments distant from the inferoseptal region. Contrastingly, maximal ECV was consistently observed in the basal and mid-ventricular inferior-septum, even in asymptomatic individuals. Segmental LS decline correlated with ECV expansion but not with native T1 values. CONCLUSION Our findings suggest that the inferoseptal segment is highly susceptible to amyloid infiltration, and 2D speckle-tracking echocardiography and CMR may serve as a valuable tool for its early detection.Citation: Toshihiro Tsuruda, Hiroshi Nakada, Yoshimasa Yamamura, Yunosuke Matsuura, Miyuki Ogata, Miyo Tanaka, Yosuke Suiko, Soichi Komaki, Hiroki Tanaka, Kohei Moribayashi, Takeshi Ideguchi, Tamasa Terada, Tomomi Ota, Keisuke Yamamoto, Kensaku Nishihira, Yoshisato Shibata, Koichi Kaikita, Basal inferoseptal segment is highly susceptible to deformation in the clinical spectrum of transthyretin-derived amyloid cardiomyopathy, European Heart Journal Open, 4(5), 2024-08-31, https://doi.org/10.1093/ehjopen/oeae07

Observation of B+ → χc0K+

journal articl

空間構成を考慮した市街地難燃化整備計画に関する基礎的研究

筑波大学University of Tsukuba博士（工学）Doctor of Philosophy in Engineering2004【要旨】著者の希望により要旨のみ公開thesi