Self-assembling DNA complexes: an in vitro platform to probe the relation between transcription and condensed DNA phases

DNA organization within a cell is multifaceted and dynamic. Not only does chromatin structure vary with position, as there is significant heterogeneity in the degree of local compaction within the global DNA complex, but it also changes with time, showing dependence on, e.g., the growth stage of a cell. The condensation state of DNA is intimately coupled to gene accessibility and expression: changes to DNA organization can modulate transcription and, in turn, transcribed RNA can reorganize chromatin structure. We sought to develop a more tractable, in vitro platform to probe this complex relationship and utilized a self-assembling DNA nanostar (NS) as the principal component of a chromatin mimic. In this dissertation, I will discuss our research with condensed phases of self-assembled NSs, describing structural properties of the system's two phases (i.e. NS-networks & NS-liquids), features of NS-liquids that enable application as a model of membraneless organelles, and initial work examining the transcription of genes integrated within NS-liquids.