Capture and Translocation of Nucleic Acids into Sub-5 nm Solid-State Nanopores - Nanopores: Sensing and Fundamental Biological Interactions - page 229

many novel approaches for nanopore-based detection of individual, unlabeled
biopolymers. The impact of these methods is twofold: First, they expand the existing
arsenal of single-molecule techniques by providing a wide variety of new means for
analyzing biopolymers. For example, nanopores have been used to differentiate
among nucleic acid (DNA or RNA) populations of varied length and sequence
[ 34 , 49 ], to probe secondary structure formation in nucleic acids [ 8 , 32 , 33 ,
40 , 46 ], to detect specific or nonspecific interactions of nucleic acids with proteins
or small molecules (i.e. drugs) [ 4 , 14 , 18 , 49 , 51 ], and to map individual transcription
factors bound to genomic DNA molecules [ 24 ]. Second, the unique ability of the
nanopore method to analyze unlabeled single biomolecules has been adapted to
engineer many novel sensing approaches for a broad range of biomedical and
biochemical applications, including genome profiling [ 41 ], single-molecule DNA
sequencing [ 5 , 9 , 42 , 43 ], and stochastic chemical sensing [ 20 , 21 ]. Nanopores have
just begun to impact scientific and technological discovery, and the next major
breakthroughs in the development of this platform hinge upon progress made in
two parallel avenues of research:

1. Development of a fundamental understanding of the dynamical processes
governing biomolecules near and inside nanoscale devices, and of the interplay
between various forces and interactions to which biomolecules are subject.
2. Availability of tools and methods allowing routine fabrication and manipulation
of materials with nanometer resolution and accuracy.

Here, we will focus primarily on current progress toward a basic description and
understanding of the fundamental physical rules governing voltage-driven biopoly-
mer transport through nanoscale pores, because it is this knowledge that uniquely
enables the development of future nanopore sensing methodologies. Over the past
decade, both large biological membrane channels, like the toxin

-hemolysin, as
well as man-made nanopores fabricated in ultra-thin solid-state membranes, have
been used to detect, characterize, and manipulate biopolymers. The quest for next
generation DNA sequencing methods has also sparked an interest in using nano-
pores for the analysis of nucleic acids, such as single- and double-stranded DNA
and RNA molecules [ 1 , 6 , 22 , 31 , 34 , 35 , 40 ]. These studies shed light on the two
equally important and essential molecular processes involved in nanopore sensing,
namely: biopolymer capture and biopolymer translocation .

a

Capture is the process by which polymers (and more specifically, polyelectrolytes)
arrive to the vicinity of the pore and are threaded into the pore. This process
determines the overall throughput of nanopore sensing. A low capture rate translates
to low throughput, which in turn limits the practicality of nanopore applications.
On the other hand, an extremely high capture rate would have profound implications
for biopolymer sensing, as this would enable the possibility for analysis of minute
amounts of sample (e.g. number of DNA copies) [ 50 ], while circumventing the need
for costly and time-consuming preamplification steps [ 5 ].

Translocation describes the dynamics of the biopolymer after it has already entered
the pore, as it is progressively transported from the source chamber (“ cis ”) to the