Chemical Society Seminar: Dr. Amani Hariri - Advancing DNA Nanotechnology Using Single Molecule Fluorescence Methodologies

DNA is a reliable and programmable nanofabrication building block. Taking advantage of its nanoscale features, I used it extensively to generate complex reconfigurable assemblies with many recent potential applications. My PhD research can be divided into four main parts: (i) synthesis optimization (Hariri et. al. 2015), (ii) structural characterization (Hariri et. al. 2017), (iii) monitoring dynamic structures (Rahbani et al. 2015), and (iv) studying structural dynamics (Platnich et. al. 2017). First, a solid-phase synthesis strategy and its visualization through SMF spectroscopy was devised to assemble nanotubes in a stepwise fashion, with a full control over their size and sequence pattern. This method paves the way for the production of custom-made DNA nanotubes with fewer structural flaws than the spontaneous-assembly method. Second, SMF photobleaching and two-color approaches were combined to provide a systematic way of assessing the polydispersity, stoichiometry and degree of defectiveness of DNA nanotubes. Third, in situ SMF was employed to introduce structural changes into DNA nanotubes by dynamically adjusting one or several of the edge lengths between the building blocks using strand displacement and loops. This is interesting for sensing applications, especially when the analyte produces large scale, detectable structural changes. Lastly, dynamics of DNA nanotubes, reconfigured in response to site-specific deletion of DNA strands, were investigated using SMF microscopy. This strategy enables to develop a better understanding of the collective structural changes within DNA structures. Together, the different methods developed underline the importance of SMF techniques as powerful tools which can advance the field of DNA nanotechnology by enabling the production of well-defined high-quality objects that can meet the designer’s compositional and dynamic specifications.

My current postdoctoral work focuses on developing real-time DNA-based biosensors: The capacity to measure specific biomolecules rapidly in vivo would provide clinicians with a valuable window into patients’ health and their response to therapeutics. The Soh lab developed the first “universal real-time biosensor technology” capable of continuously tracking a wide range of circulating molecules in living animals (Mage et. al. 2017). This real-time biosensor requires no exogenous reagents, operates at room temperature, and can be reconfigured to measure a wide range of target molecules by exchanging probes in a modular manner. At the heart of the sensor is an aptamer probe, which is labeled with a redox reporter and immobilized onto an electrode within a microfabricated device. These aptamer probes fold reversibly, enabling continuous tracking of rising and falling concentrations of the biomarker in real-time. Importantly, the aptamer probe governs the sensor’s sensitivity, specificity and temporal resolution. The Soh Lab has achieved many milestones in the development of advanced techniques that are now in widespread use for aptamer discovery, including the click particle display (click-PD) method which allows for the high-throughput screening and isolation of chemically modified, non-natural aptamers (Wang et. al. 2016).