Nanomaterials and chip‐based nanostructures for capillary electrophoretic separations of DNA

Abstract

Capillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) using polymer solutions are two of the most powerful techniques for the analysis of DNA. Problems, such as the difficulty of filling polymer solution to small separation channels, recovering DNA, and narrow separation size ranges, have put a pressure on developing new techniques for DNA analysis. In this review, we deal with DNA separation using chip-based nanostructures and nanomaterials in CE and MCE. On the basis of the dependence of the mobility of DNA molecules on the size and shape of nanostructures, several unique chip-based devices have been developed for the separation of DNA, particularly for long DNA molecules. Unlike conventional CE and MCE methods, sieving matrices are not required when using nanostructures. Filling extremely low-viscosity nanomaterials in the presence and absence of polymer solutions to small separation channels is an alternative for the separations of DNA from several base pairs (bp) to tens kbp. The advantages and shortages of the use of nanostructured devices and nanomaterials for DNA separation are carefully addressed with respect to speed, resolution, reproducibility, costs, and operation.

Strong effects of molecular topology on diffusion of entangled DNA molecules

“…However, with Ϸ40-to 300-kbp fosmids and bacterial artificial chromosomes the linear form migrates the fastest followed by the supercoiled, whereas the mobility of the relaxed circle is practically zero (37,38). More recently, fabricated nanostructures have been used to study transport and conformation of single DNA molecules of different lengths and topologies and have led to many insights into their dynamics in confined environments (39)(40)(41). The reptation model was originally used to explain DNA mobility in both DC and pulsed-field gel electrophoresis as well as other confined environments; however, predictions did not always match experiment, and further contributions and corrections were needed to account for observed motion (34).…”

Nanofluidic structures for single biomolecule fluorescent detection

“…[36][37][38] A single DNA strand may be visualized as it interacts with pillars in a microfluidic slit, [39][40][41] or as it escapes from a deep well into a thin slit, and it is hoped that the knowledge gained from such studies will lead to faster methods of lab-on-chip DNA sorting. [42][43][44][45][46][47][48] Finally, sequence information may even be obtained from stretched molecules through restriction site mapping or motif mapping using hybridized probes. 19,20,49 In addition to stretching via hydrodynamic forces, channels, planar slits, and pillar arrays, fabricated into glass or silicon wafers can also be used to study the mechanical dynamics of a DNA molecule by employing entropic forces that arise due to confinement.…”

Genotyping with microfluidic devices

“…System integration led to the 'lab-on-a-chip' concept with such multiple functions as PCR amplification, restriction digestion, separation, fraction collection, etc [10]. The progress in the field was summarized in several reviews in the past few years [9,[11][12][13][14][15][16][17][18][19][20][21].…”