Capture and Translocation of Nucleic Acids into Sub-5 nm Solid-State Nanopores - Nanopores: Sensing and Fundamental Biological Interactions - page 228

10.1 Introduction: Biopolymer Translocation

Through Narrow Pores

Resistive sensing is based on monitoring changes in the ionic conductance through
micrometer-scale apertures during the passage of colloidal particles (i.e. cells). This
method, also known as “Coulter counting,” has been broadly applied across the life
sciences and biochemistry [ 10 ]. The nanopore method employs a similar detection
principle, but uses an aperture that is only a few nanometers wide - suitable for
probing individual molecules [ 11 , 15 , 48 ]. Another crucial difference between
classical particle counters and nanopores is the ability of the latter to linearize long
polymer coils during detection (Fig. 10.1 )[ 49 ]. Consider a long biopolymer (e.g. DNA
or RNA) with chain cross section a ,andananoporeofdiameter d , where d is only
slightly larger than a and is much smaller than the polymer's coil size, commonly
estimated by its radius of gyration r g ( a<d ¼ r g ). When this biopolymer is threaded
through the nanopore, its equilibrium coil structure must be deformed and linearized
by the narrow constriction. Thus, the ionic conductance of the blocked nanopore
can be directly related to local characteristics of the linearized biopolymer. This
powerful feature sets the nanopore method apart from most other sensing methods,
and makes it particularly useful for analysis of long biopolymers, particularly nucleic
acids [ 1 , 22 , 33 , 34 ]. It is therefore anticipated that nanopore-based platforms will be
developed as future-generation tools for genomic profiling and for DNA sequencing,
where the ability to linearly analyze long biopolymers ranging from thousands to
hundreds of thousands of base pairs in length is particularly advantageous [ 5 ].
The ability to experimentally analyze individual molecules during transit through
nanopores has greatly contributed to our basic understanding of the physical pro-
cesses governing biopolymer transport. This, in turn, has led to the development of

Fig. 10.1 The principle of resistive sensing. Left panel : Illustration of Coulter counter. An electric
field draws charged particles through a micrometer-scale aperture in a membrane separating two
salt buffer-filled chambers. Particles are detected and counted as they occlude this opening during
their passage, blocking the flow of ions through the pore and producing a transient drop in current.
Right panel : Illustration of nanopore setup. The applied voltage forces long, charged biopolymers
to translocate linearly through a nanoscale pore. Molecules are both detected and characterized by
the resulting transient changes in current through the nanopore