Seeman Student Travel Awards at DNA30

Kanta Takagi, Tokyo Institute of Technology, Japan
In our research, we constructed a programmable computational droplet system that can realize and control the dynamic behaviors of DNA droplets based on information processing. By designing DNA nanostar sequences, we achieved computational DNA droplets that can perform an AND operation accepting two single-stranded DNA as inputs. Only when the two input are present, the DNA droplets are dissolved by breaking the DNA nanostars through DNA strand-displacement reactions. The diffusion of dissolved DNA nanostars generates a hydrodynamic flow, allowing the movement of the DNA droplets. The concept of this system strongly relates to Dr. Seeman’s vision defined as “controlling matter with chemical information.” Our system demonstrates that not only controlling the nanostructures such as DNA tiles and DNA origami but also controlling microstructures called DNA coacervates with chemical information processing based on DNA computing strategy. We believe this system will significantly contribute to the extension of the concept of controlling matter.

Qi Yang, Rutgers University-Newark, USA
Our research on RNA tiles to develop programmable systems for RNA assembly and sensing aligns with Professor Seeman’s pioneering vision of “controlling matter with chemical information”. Building on Seeman’s foundational contributions to nucleic acid nanotechnology, particularly the assembly of larger patterns using tiles, we explore the design of novel RNA tiles and applications of RNA nanostructures. We introduced a new class of RNA tiles incorporating antiparallel crossovers and T-junctions—structural elements originally developed in DNA nanotechnology—to create diverse one- and two-dimensional assemblies. We created 21 distinct tiles, significantly expanding the collection of multi-stranded RNA tiles. We also demonstrated the integration of split broccoli RNA aptamers into the structures, enabling fluorescence activation along linear arrays for programmable RNA sensing. The incorporation of functional RNA highlights the vast potential of these RNA tiles in constructing advanced nanostructures for biomaterial applications.

Sreelakshmi Meppat, University of Sydney, Australia
Our research aims to develop switchable DNA origami nanopores capable of controlled interaction with cell membranes. Our system consists of a DNA nanopore encapsulated in a DNA origami barrel. This approach provides enhanced control over the interaction between the nanopore and the membrane by decoupling membrane docking from membrane insertion. We have shown how toehold-mediated strand displacement can initiate the release of the nanopore from the barrel cavity, allowing the nanopore to insert into a lipid bilayer. By modifying the structural design, in the future this nanopore system can be tuned to react to different chemical signals, such as pH levels, light, or other biochemical cues, thereby enabling applications in targeted drug delivery and beyond. The dynamic and customizable nature of our nanopore design, controlled by chemical signals, embody Ned Seeman’s vision of programmable DNA-based nanostructures.

Taryn Imamura, Carnegie Mellon University, USA
My research extends Dr. Seeman’s vision into the realm of microrobotics by using the properties of DNA to construct physically intelligent micro-swimmers with programmable behavior. By combining microspheres with DNA nanostructures, we have constructed modular microrobots that locomote, but cannot directly sense and respond to their environment. My goal is to use the programmable and responsive properties of DNA to give these microrobots the sensing, signaling, and cargo-carrying capabilities needed to autonomously execute tasks. My research establishes a framework for manufacturing and characterizing populations of customizable DNA-microsphere hybrid structures and provides the first baseline assessment of their response to magnetic and chemical stimuli. Much like Dr. Seeman’s foundational work on extending DNA crossovers to form larger crystaline structures, I aim to study how DNA nanostructure properties impact microswimmer agility and functionality, eventually extending these principles to develop complex microrobot systems that are controllable, programmable, and responsive to their local environment.

Thong Diep, Arizona State University, USA
Leveraging Ned Seeman’s vision of using DNA to control material assembly, we developed an integrated platform that combines computational modeling, algorithmic design, and DNA nanotechnology to establish a universal design pipeline for desired 3D nanostructures. The inverse design of the target structure is realized through ‘SAT-assembly’, where the converted Boolean Satisfiability Problems are solved for an optimized interaction matrix and a minimal number of building blocks without kinetic traps in self-assembly. Produced designs are implemented in DNA origami and further validated using a coarse-grained model (oxDNA) in molecular dynamics simulations before experimental realization. We experimentally demonstrate a range of assemblies with different sizes and complexity, such as lattices, capsids, and polycube objects, including multifarious assemblies where the same particles can form multiple different target assemblies, as well as dynamically reconfigurable structures. The proposed pipeline based on optimized algorithms and simulations will represent a valuable tool for the DNA nanotechnology community.

Tiernan Kennedy, University of Washington, USA
Modern electronic computers are currently unmatched in their capacity for general-purpose information processing. In fields like biomedicine and biomanufacturing, molecular information is typically sampled, assayed, and then processed by conventional computers. These processes are often manual, time consuming, and may take place across multiple locations. Processing information directly at the molecular scale streamlines these processes, reducing the demand for specialized labor, even without the high speed of electronic computation. However, achieving operational fidelity with molecular circuits remains a challenge. Our work addresses one aspect of this issue by improving circuit performance in biological environments, like cellular RNA extracts, through systematically incorporating non-natural nucleotides to reduce interactions with kinetically interfering background molecules. This development broadens access to chemical information processing and brings us closer to realizing Ned Seeman’s vision of molecular information processing systems with complex, societally impactful applications.

Yi-Xuan Lee, National Taiwan University, Taiwan
Our work focuses on exploring the potential of surface chemical reaction networks (sCRNs), a programmable model proposed to use DNA as a building material. We investigate its pattern-creating capabilities by comparing it to the established self-assembly model, aTAM, introduced by Winfree and utilizing DNA tiles designed by Seeman. Research on aTAM has shown that pattern formation and programmability are complementary. Leveraging these insights, we theoretically guarantee the pattern formation capabilities of sCRNs through precise molecular control. Given the local nature of molecular transitions in sCRNs, our study also examines their ability to perform dynamic spatial arrangements. We explore the connection between sCRNs and other active models that update patterns based on local information. This approach aligns with Seeman’s research on implementing cellular automata-like arrangements using DNA tiles and other work on DNA models capable of designated local transitions.