Feedback Control of Biological Polymers in a Nanopore

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DESCRIPTION (provided by applicant): Electronic sequencing in nanopores shows great promise for inexpensive DNA sequencing at high speed and with minimal preparative steps. Such capability would lead to efficient reading of human SNPs or other genetic variations, which would in turn have a significant impact in pharmacogenomics and other disease treatments and preventions based on information from the patient's own genome. Recently, researchers identified the inability to regulate the speed of a molecule's translocation through the pore as the primary obstacle to realizing the sequencing potential of hemolysin nanopores. The proposed research will investigate the application of feedback control to substantially improve the ability to regulate molecule translocation speeds in a nanopore, thereby improving the ability to sequence with existing nanopore technology. In particular, the primary goal is to design novel hardware and software algorithms for feedback control of single polymers in a hemolysin nanopore on a microsecond time scale and with near angstrom precision. Such capability would contribute to the development of nanopore-based sequencing technologies, augment the efforts of the $1000/mammalian genome project, and be a revolutionary contribution to the realm of applied feedback control. The control algorithms would also leverage the long-term objective of the proposed effort: the development of a nanopore-based single cell analyzer. The device would enable one to efficiently determine the concentration of all mRNA in a single cell at an instant of time. This technology would improve the ability to accurately track molecular events that occur during cell differentiation, by reducing the number of cells required for event detection and increasing the time resolution of detection measurements. There are two primary aspects to the proposed research program that are necessary augmentations to my expertise in control. First, I will engage in a two-year intensive period of didactic training in relevant courses, including molecular and cellular biology, embryology, cell signaling, genomics and bioinformatics. The basic understanding gained is required for success in the application of control to problems in human health broadly, and in technology development for cell interrogation specifically. Second, I will participate in the $1000/mammalian genome project to learn about the physics and biology of the hemolysin nanopore. In parallel to the $1000 genome project, I will explore the controlled capabilities of the nanopore for efficient mRNA sequencing, using tools from bioinformatics and machine learning to translate the controlled response data into the identity of unknown nucleotides.