ABSTRACT
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 micro-
scopy,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 inter-
action 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 solid-
state nanoscale pores24-33 that can detect DNA and that may have utility in high-speed DNA sequencing.
The concept underlying nanopore analysis of DNA is simple: individual nucleic acid molecules are
detected as each strand threads through a nanometer-scale opening between two aqueous chambers,
typically driven by an applied voltage (Figure 11.1). Two features distinguish nanopore DNA detectors
from more conventional DNA detection methods: (i) DNA is sampled directly from bulk-phase solution
with no labeling or modification, and (ii) DNA is examined one molecule at a time. Most techniques
used to detect DNA amplify the sequence information to a detectable level by using labeling, polymerase
chain reaction (PCR), or adhesion to a surface-active detector.34,35 Even techniques used to examine
