Nanoscale DNA analysis

Microchip electrophoresis has been developed as a promising technology for detection of DNA in samples.^1-3 However, the development of systems for the separation of long DNA strands [greater than several kilo basepairs (kbps)] using commercially available media, has not been successful.⁴ In recent years, efforts have been focused on the overcoming the limitations of current DNA electrophoresis methods. Those limitations largely result from an application base that only required the separation of DNA fragments in a narrow size range, one where using fundamental separation modes based on sieving using conventional methods.⁵ In conventional gel electrophoresis, DNA molecules move in the electric field based on a size-dependent mobility through pores in a gel matrix.⁶ However, length-dependent mobility vanishes for DNA molecules longer than 40 kbps, primarily due to tendency of DNA molecules to become stretched and oriented to the direction of electric field.^7,8 Buoyed by the knowledge of micro- and nanofabrication technologies, nanotechnology has been shown to be quite successful for long fragment DNA analysis. To achieve the required efficiency needed for this type of DNA electrophoresis, two directions in the field of nanotechnology have been established: one focused on providing artificial gel structures produced with nanofabrication technology, and the other on nanomaterials for DNA separation. In this chapter, we discuss the developments and capabilities of nanoscale methods for DNA electrophoresis, and provide some important technical information for each method. Considering the point that the mechanism of DNA separation in each nanotechnique is different (and sometimes unique) from other better-understood separation modes, these will be explained separately.