(549e) The Role of Order in DNA Separations in Colloidal Crystals

The advances in microfluidic separations of biomolecules such as DNA rely in many ways on the fabrication of the devices.  Photolithographic techniques allow for detailed structures to be patterned over large areas in very repeatable locations, leading to highly ordered devices.  These techniques fall under the moniker of “top-down” fabrication.  If instead of photopatterning and etching one uses self-assembly, the technique is considered “bottom-up”.  These devices are less deterministic in their structure, and therefore not as precisely ordered.  And, until now, it has been unknown whether the order of the system is important to the separation efficacy.

We have developed an analytical setup that is capable of measuring both the local order properties as well as DNA separation performance as a function of position in the device.  We use self-assembled colloidal crystals as a sieving matrix, as they are capable of forming structures with either long-range order (large grain size) and short-range order (smaller grains).  By carefully controlling the crystal growth rate, we can tune the location of long- and short-range order in the device.  We qualitatively measure the locations of these regions using white light Bragg diffraction imaging and quantitatively measure the order using small angle laser light diffraction.

After characterizing the colloidal crystal, we then use the device to separate a known mixture of DNA.   We rapidly scan the channel, taking measurements of the dyed DNA’s fluoresced intensity versus position in the channel with a small time interval in between measurements.  We use the large data pool to then create pseudo-finish line experiments, showing us the separation performance at arbitrary elution lengths without needing to perform the numerous separate experiments.

By combining the measurements of the order and the DNA separation, we are able to show that order does play a role in the separation power of the device.  Long-range order is shown to have nearly double the separation power of short-range order colloidal crystals.  This analytical setup is key in understanding the effect local properties in heterogeneous separation media have on the separation of biomolecules.