Johns Hopkins University
To understand the basic properties of biomolecular condensates based on DNA/RNA and to control condensate properties, interactions, and dynamic responses using nucleic acid circuits
Compartments, i.e., discrete spatial regions, are important to life. Cells use them to store molecules for later use and to promote biochemistry by keeping molecules close to one another. Life typically compartmentalizes via walls built from lipid membranes, but biologists have discovered that life also employs a membrane-free approach to compartmentalization. Rather than relying on a wall to demarcate what's inside vs outside of a compartment, life can instead employ phase-transitions, changes in the state of matter (e.g., liquid or solid), to segregate molecules. Envision a gel-like region of closely interacting chemicals within a large liquid-like region of a cell. These phase-change compartments are called biomolecular condensates. They are ubiquitous in living systems and important to cellular function. Condensates have been identified that sequester damaged proteins and orchestrate chromosome separation during cell division, and they've also been implicated in human diseases such as Alzheimer’s. This grant funds work by a team led by Rebecca Shulman at Johns Hopkins University who are attempting to understand and ultimately control condensates as a step towards an improved understanding of compartmentalization that could shed light on the matter-to-life transition. Condensates appear well-positioned for this purpose. On the one hand they share many core functions with cells. Condensates naturally form, grow, dissolve, fuse, and divide. On the other, they are vastly simpler, biomechanically, than cells themselves, allowing researchers to investigate these core activities without the complicating internal structure present in natural cells. The work will focus on nucleic acid-based condensates, condensates where the nucleic acid polymers DNA and RNA are the functional elements that condense or otherwise control the phase transition between a condensate and its exterior. The team's approach is to design, build, and characterize nucleic acid condensates. They'll design synthetic DNA templates that produce RNA molecules with the capacity for spontaneous phase separation, testing hypotheses about how aspects of polymer design influence the condensation process. They'll use optical microscopes and other tools to achieve high-throughput characterization that leads to phase diagrams that summarize condensate properties under varying conditions (temperature, different condensing macromolecules, various solution-phase buffer-molecules). They'll also develop molecular signals that cause distinct condensates to mix or demix with one another, or which cause one type of condensate to expel molecules that signal another condensate to perform some function. These studies will provide insights into how condensates can be used to transport "cargo," chemicals that are not essential to the condensation itself but are instead stored or transported by the condensate. If successful, the project could form the foundation of a new discipline of condensate engineering, one that could open new routes to chemical synthesis, advance our understanding of natural cells, lead to new types of intracellular organelles, and provide insights into how matter transitions to life.