Physics of Confined DNA

Polyelectrolyte Physics under Confinement

Our lab is interested in the basic physics of nanoconfined polymers. To this end we place DNA into nanofabricated channels and mazes and observed it motion either under at equilibrium or under and applied stress:

DNA collapses in an electric field

DNA is a polyelectrolyte, meaning it is a charged molecule when placed into acqueous solution. Many traditional theories assume a linear respone of polyelectrolytes to electric fields. We show that this is probably incorrect since linear theories predict that polyelectrolytes stretch in electric fields. We have discovered that they instead collapse when the electric field strength is increased above a threshold. We are currently exploring the interaction of counter-ions, co-ions, and polyelectrolytes at high electric fields. In the image below, DNA is placed into a microchannel and a voltage of a 700 V/cm is applied at 300 Hz (scale bar 5 microns).

DNA flucutates as a harmonic oscillator chain when confined to a channel

The classical view of polymer diffusion in solids and very dense suspension is called reptation. It assumes that the polymer cannot move sideways, but rather moves along its backbone like a snake sliding through grass. It thus moves in a channel, and an important question is how it fluctuates inside the channel. We show that on scales larger than the length-scale of the smallest chain with self-avoidance (in the free Flory picture), a simple overdamped harmonic oscillator chain captures all of the physical properties. In particular, we are able to detect the presence of Rouse modes that behave as if they were free-draining (an effect of hydrodynamic screening in nanofluidics).

Onset of herniation observerd on molecule in nanochannel maze

The reptation picture above is typically incomplete for describing the motion of a polymer through a solid or a dense solution because there are many possible reptation channels for the polymer to explore. This exploration could occur not onle at the leading end (head), but also in the middle. This process is termed herniation. We have observed that there is a critical driving force for herniation to occur in a regular lattice of nanochannels. We further showed that this threshold is an effect of the excluded volume of two chains occupying the same channel segment. In the image below we show the migration of a megabase-DNA chain through a lattice with 100 nm-wide channels. The molecule is linear!!