(162j) Single Molecule Studies of DNA Collapse in Slit-Like Confinement

Single molecule experiments of DNA in the presence of condensing agents have informed scientists about the high density packing of DNA in biological systems.  Typically, these studies are performed in unconfined, in vitro environments with condensing agents such as multivalent cationic species (e.g. spermine³⁺, Co(NH₃)₆³⁺).  However, relatively little attention has been given to single molecule DNA collapse in weaker condensing agents, such as ethanol.  Moreover, studies on the effects of restricting DNA conformational space (e.g. via confinement) on kinetics of collapse are nearly non-existent.   In this talk, we will discuss our experiments with single molecules of dsDNA in the presence of ethanol and confined to slit-like nanochannels.  The compact states induced at our ethanol concentration (and in bulk) are shown to be much larger and amorphous than the highly condensed, orderly toroids seen in multivalent cation induced DNA collapse.  We attribute this difference to the long lived, higher order intermediate racquet states that one sees when collapsing semiflexible chains in poor solvents.  Furthermore, we study the kinetics of collapse of individual DNA molecules.  We find that the collapse is a two step process much like a nucleation-propagation event.  More strikingly, we observe that the time to collapse DNA is reduced by an order of magnitude, relative to bulk, when confining DNA to slit-like nanochannels.  This behavior is further explained via scaling arguments.  We believe these results will have future relevance in single molecule assays and biological physics.