Nanoscale pores can be used to examine the structure and dynamics of individual DNA or RNA molecules. Compared to other single-molecule techniques (e.g., optical tweezers,1 atomic force microscopy,2 and fluorescence energy transfer3), nanopore detection techniques are unique in their ability to rapidly sample nucleic acid from solution. This chapter will focus on DNA detection experiments using the protein ion channel a-hemolysin. Single-molecule DNA detection using ionic current measurements was first demonstrated using this nanopore detector prototype4-9 (for review of the biophysical properties, see Meller10). Subsequent technical improvements revealed sequence-dependent DNA interaction with the a-hemolysin pore.11-23 However, the biological detector lacks the robustness required for a standardized analytical instrument. To address this issue, several investigators are developing solidstate nanoscale pores24-33 that can detect DNA and that may have utility in high-speed DNA sequencing.

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