Seminar: Dynamic Control of DNA Structures

Written by: Karmella Haynes. Tonight, Elisa Franco from University of California, Riverside presented her work on “Bottom up construction of biomolecular materials.” Her group’s overall approach is to integrate layers of nucleic acid-based devices.

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Elisa’s goal is to couple an oscillator with self-assembling DNA nanotubes. The nanotubes assemble and disassemble at the low and high points of the oscillations. Connecting something with dynamic behavior, like an oscillator, to nucleic acid assembly has many challenges, such as differences in time scales, length scales, signal transmission, and environmental compatibility.

Elisa’s group designed nucleic acid to mimic microtubules, and called these structures nanotubules. Currently, all of the experiments are carried out in a defined, in vitro environment, thus “no cells were harmed during the collection of data.” The defined system allowed the group to develop mathematical models to design and simulate the system.

In order to model and control the dynamics of nucleic acids, Elisa’s group used toehold mediated branch migration. Conformational changes were induced by Watson-Crick base-pairing-mediated displacement. For instance, where A + B are complexed, C will displace A if C has more complementarity with B than A has with B. This design was used to control the activity of a promoter at a reporter gene. Direct control of nucleic acid function via toehold switching helped to circumvent the translation pathway (before the gene activation step), and to avoid undesired complexity.

Although the group was able to generate ultra-sensitive switches with oscillating behavior (where fluorescence was the output signal), they observed a lot of variability in the results, even when the same person repeated the experiment with the same reagents, but just on a different day. In order to reduce variability, they used micro droplets of oil to encapsulate the oscillator. Imaging experiments revealed oil droplets lighting up and growing dim as the device inside the droplets oscillated. This allowed the group to dramatically scale-up replicates and collect enough data to discover the source of variability. Interestingly, the culprit was the diameter that encapsulated the oscillator. Elisa proposed that the volume of the reaction impacted enzymatic losses (degradation). The take-home lesson was that when you encapsulate a dynamic system, you must pay attention to enzymatic losses, which will cause variability in period and amplitude and disrupt the behavior of the system.

Elisa’s long-term goal is to couple an optimized, robust micro-scale oscillator with DNA nanotube formation to drive pulsed behavior of the material. She hopes to translate this tool to larger, more complex structures, such as objects built from DNA origami. As other self-assembling materials become available, they might also be controlled by micro-oscillators.

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