Synthetic biology can provide solutions for pressing challenges and redirect our ways to understand life. The ability to designing biological systems is dependent on the ability to regulate gene expression. Nucleic acids open new avenues for artificial gene regulators owing to the programmability, versatility, low genetic footprint, and economic production. In this talk, applications of nucleic acid-based synthetic biology for metabolic engineering and biomedical engineering will be introduced. First, I am going to show examples on how to develop nucleic acid-based gene regulators for metabolite-sensing applications. Specifically, a new approach for the development of RNA switches and their application to guide the evolution of metabolite-producing recombinant bacteria will be presented. Then, an example demonstrating how to develop a cell-free gene expression system based on DNA probes for molecular diagnosis will be introduced. Specifically, a rationally designed nucleic acid-based platform for rapid diagnosis of pathogens will be presented.

A longstanding proposal claims that electrodynamical interactions can play an essential role in the dynamical organization of biological systems at molecular scales. In other words, long-range electrodynamical interactions between resonant oscillating dipoles can facilitate the encounters of cognate partners of reactions. In such a framework, I present some theoretical, numerical, and experimental results on the research of the existence of classical electrodynamic interactions when biomolecules are excited and brought out of thermal equilibrium. In particular, we show some evidence of the excitation of giant dipole oscillation in biomolecules and the consequent activation of long-range forces among them.

The quantum nature of the electromagnetic field have proven for many years to be extremely rich from an information processing point of view, and more recently for offering a new perspective on quantum computation. After giving a brief review of the core aspects of ‘continuous-variable quantum computation’, we illustrate how photonic circuits offer a natural playground to study Coulomb-coupled Drude oscillator-based models of long-range intermolecular interactions.

Water freezing is a commonly observed natural phenomenon; however, ice growth and recrystallization can critically damage living organisms. Nature has evolved to produce antifreeze proteins (AFPs) to survive this freezing threat. Their specific amino acid sequence has been widely accepted to play a critical role in binding to ice, which can result in antifreeze activity when the Kelvin effect is dominant at the ice interface. On the contrary, ice-binding surfaces can also lead to heterogeneous ice nucleation when the appropriate chemical and dimensional aspects are satisfied. Ice nucleation proteins and their mimics possess relatively large ice binding surfaces, which facilitates the organization of surrounding water molecules in an ice-like lattice that could promote ice nucleation. Both phenomena, which require ice-binding characteristics in common, demand distinct design protocols, and thus active materials have been developed by tailoring them for respective purposes. In this presentation, mimicking the unique ice-activity of proteins, we will address our recent achievements [1-5] based on tailored designs of the hydrogen-bonding nature at the water-ice interface enabled by assemblies and macromolecules with topological engineering.

Understanding the emergence of dynamical facilitation is central to glassy behavior in supercooled liquids. Dynamical facilitation refers to the phenomenon where motion in one region triggers motion in another, leading to spatially correlated dynamics. Here, we present a theory that reveals the microscopic origin of dynamical facilitation. We show that the interaction between a localized bond exchange event (excitation) and elastic stresses accumulated by prior excitations leads to emergent facilitation and glassy dynamics. Using the theory of linear elasticity and Markov processes, we simulate a model, which reproduces multiple aspects of glassy dynamics observed in experiments and molecular simulations, including the stretched exponential decay of relaxation functions, the super Arrhenius behavior of relaxation timescales as well as their two-dimensional finite-size effects. These results show how the elastic nature of excitations and their interactions leads to a self-consistent microscopic picture of glassy dynamics.

Imposing strong quantum confinement in lead halide perovskite quantum dots enhances the electronic interactions of charge carriers and dopant spin within the quantum dot and promotes the delocalization of the exciton among the quantum dots in the close-packed quantum dot ensemble. Enhancing intra-quantum dot exciton-dopant interaction and inter-quantum exciton coupling in strong confinement regime can enhance the capability of perovskite quantum dots as the source of the Auger-upconverted hot electrons and cooperative photon emission as superradiance. Here, I will discuss (i) the generation of hot electrons via Auger upconversion involving long-lived dopant state in strongly quantum-confined cesium lead bromide (CsPbBr3) quantum dots doped with Mn2+ and (ii) the cooperative photon emission as the superradiance from the electronically coupled quantum dots in superlattice. Strong confinement that enhances exciton-dopant interaction proved to enhance the effectiveness of hot electron generation via Auger process that could also take advantage of accessible long-lived dark exciton state at low temperature for upconversion process. The superlattice of CsPbBr3 quantum dots, where the electronic coupling is enhanced by imposing strong quantum confinement and reducing facet-to-facet distance, produced the superradiance that exhibits linear polarization indicating the ability to introduce anisotropic electronic coupling in the superlattice formed from CsPbBr3 quantum dots.

Transcription is the first step of gene expression; therefore, it is highly regulated either by trans-elements like protein factors and/or by cis-elements like specific sequences on the DNA. In the early stage of infection, lambdoid phage HK022 transcribes a cis-element, put RNA, which suppresses pausing and termination, facilitating the phage infection. The put transcript solely performs the anti-pausing/termination activities without an additional protein factor and directly interacts with the E.coli RNA polymerase elongation complex (EC) by an unknown mechanism. In this study, we reconstituted put-associated ECs and determined the structures using cryo-electron microscopy. The assembled complexes consisted of put-associated EC, put absent EC, and σ70-bound EC, and their structures suggested that the put binding to the EC counteracts swiveling, thereby inhibiting transcriptional pausing. Furthermore, we observed that σ70 binding promotes the folding of put, suggesting a role of σ70 during elongation.

Single-molecule studies have revolutionized our ability to observe and analyze interactions between biomolecules, deepening our understanding of complex biological processes. Here, I will present the research I have conducted throughout my PhD and postdoctoral studies. During my PhD studies, I investigated the structural roles of Cas9:gRNA:DNA complex in off-target discrimination. Using single-molecule FRET in simplified reconstituted systems, I discovered that the Cas9 complex undergoes a series of structural changes during nuclease activation. Importantly, the formation of an intermediate Cas9 structure plays a crucial role in preventing off-target DNA cleavage. As a postdoctoral researcher, I am leveraging my expertise in single-molecule spectroscopy to investigate the mechanisms of eukaryotic DNA replication and repair processes, which involve a large network of interactions among hundreds of proteins. To this end, I use nuclear extracts prepared from Xenopus laevis eggs, which are believed to contain all the essential components required to efficiently perform DNA replication and repair machineries outside of a cellular context. By combining biochemical and single molecule assays with nuclear extracts, I am exploring how cells respond to replication stress. Focusing on the recently discovered mechanism of “Repriming” and its key component, PrimPol, I will present insights into how PrimPol is recruited to stalled replication forks and how its repriming activity is regulated.