Using Self-Assembling DNA Complexes to Examine the Relationship between DNA Organization and Transcriptional Efficiency

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, e.g. showing dependence on the growth stage of a cell. Much of this variability is presumed to arise through diverse, non-equilibrium interactions with proteins, whose binding dynamics and motor activities can, e.g., propagate forces throughout the weakly-crosslinked DNA network. As DNA organization is innately coupled to gene accessibility, the structural changes induced by active processes are expected to have important effects on gene expression. To begin probing this incredibly complex relationship, we use a simple in vitro system – comprised of self-assembling DNA nanostars, DNA gene templates, and RNA polymerase – to examine how transcriptional activity influences DNA organization and, conversely, how DNA structure can modulate genetic output.