Interdisciplinary Applied Mathematics

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Another application in which nanoflows are gaining considerable attention is the translocation of deoxyribonucleic acid (DNA) through a


nanopore. Functional analysis of the genome will require sequencing the DNA of many organisms, and nanometer-scale pores are being explored for DNA sequencing and analysis. The characteristic that makes nanopores useful for    analysis    of    DNA    or    other individual    macromolecules    is    that    the


scale of the pores is the same as that of the molecules of interest. For example, the diameter of single-stranded DNA (ssDNA) is approximately 1.3 nm, while the diameter of the narrowest restriction in a-haemolysin protein, the most commonly used organic pore for DNA analysis, is approximately 1.5 nm (Nakane    et    al.,    2003;    Kasianowicz    et    al.,    1996). Although    natural    ion


channels have many desired properties for sensing and analysis of macromolecules, they usually work only in carefully controlled conditions and are difficult to integrate with other components of a device. As a result, there has been a significant amount of work devoted to building robust and easy-to-integrate sensing and analysis devices based on synthetic nanopores (Li et al., 2001). Figure 1.26 shows the schematic of a nanopore-based DNA sequencing system. The basic idea is that as a DNA molecule is pulled through the nanopore immersed in an electrolyte solution by an external electric field, the partial charges on the DNA, which are different for different DNA sequences, will change the electric current through the pore. The observed current variation will serve as a signature to differentiate various DNA sequences. The diameter of the nanopore must be sufficiently small (typically less than 5 nanometers) so that the electric current can be sensitive to the DNA molecule passage. Since a nanopore device needs only a few DNA molecules to obtain reliable results, it can be much cheaper and faster compared to the traditional fluorescence-based detection schemes, in which much of the time and cost are devoted to making copies and purifying the DNA molecules so as to obtain a reasonable signal-to-noise ratio.

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