Genetic information plays an increasingly important role in life sciences and medicine today. The ultimate goal of my Ph.D. project was to develop a nanopore-based DNA sequencing device that could drastically reduce the cost of acquiring genetic information. Chapter 1 is an overview of DNA sequencing methods, including the Sanger dideoxy-termination method and many emerging "next-generation" approaches. The potential of the nanopore DNA sequencing concept, as well as the requirements that need to be met for turning it into reality, are discussed at the end. Chapter 2 starts with an introduction to the biochemical and biophysical features of the most widely used protein (alphaHL) in the nanopore DNA sequencing field. It is followed by describing proof-of-principle experiments that suggest the feasibility of the nanopore DNA sequencing concept. More specifically, the pseudorotaxane design demonstrated that single-nucleotide variations in an intact ssDNA can be recognized, and the rotaxane design demonstrated that the natural DNA polymerase motor function can be employed to effect oligonucleotide translocation in unidirectional single-nucleotide steps. Chapter 3 begins with the discussion of a previously overlooked configuration dynamics associated with the alphaHL•DNA-PEGphos rotaxane. Such a dynamic feature of the rotaxane allows us to control and monitor oligonucleotide strand translocation in real-time. While DNA polymerase remains integral to most DNA sequencing methods, we came full circle by presenting preliminary data showing that the high spatial and temporal resolution of this rotaxane system provide the means for mechanistic studies of the DNA polymerase at the single-molecule level. Chapter 4 touches upon the importance of read-length in genome-scale sequencing, and the potential impact of the nanopore DNA sequencing method in this area of research.
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