Chapter 14
DNA transport and analysis

Microdevices for analyzing deoxyribonucleic acid(DNA) are ubiquitous in biological analysis, and techniques for analyzing DNA in microchips pervade the analytical chemistry literature. Use of nanochannels to study polymer physics has also become common. Owing to DNA’s huge biological importance, its chemical properties have been thoroughly studied, and the experimental tools available for chemical analysis of DNA are numerous. The ubiquity and convenience of DNA has also led to extensive study of its physical properties. DNA is therefore an excellent example of how microscale systems facilitate analysis, as well as a model system for examining the effect of nanostructured devices on molecular transport of linear polyelectrolytes. Because the chemistry for fluorescently labeling DNA is relatively inexpensive and available commercially, fluorescence microscopy of DNA is a widely-used means for visualizing DNA. It is quite routine to fluorescently label and observe the gross morphology of a single DNA molecule with 1-μm resolution, and thus straightforward experiments can be brought to bear on questions of molecular configuration.

DNA (and other idealized linear polymers) behave physically somewhere in between small molecules (which behave like point particles) and particles (which behave like rigid continuous solid phases). The behavior observed (and the models that describe this behavior) incorporates aspects of point-like and particle-like behavior, and these behaviors are different depending on the type of transport. When we consider DNA behavior within domains (e.g., micro- or nanochannels) that are small compared to the characteristic size of the DNA molecule, these models must be augmented with explicit consideration of surface interactions. Thus, the interaction between the molecule and the confining boundaries requires some sort of physical model of the system that goes beyond typical bulk properties.

This chapter first describes the physicochemical structure of DNA, with particular attention to the mathematical description of the backbone of linear polyelectrolytes. This treatment of linear polyelectrolytes applies to DNA, but also a wide variety of other molecules whose backbones have no branched structure. Experimental observations of the bulk properties of DNA are then presented, and interpreted in the context of physical models for DNA dynamics. These models then lead to discussion of the behavior of DNA in confining domains. The behavior of DNA translates directly to applications in micro- and nanofluidic devices—bulk diffusion affects the performance of DNA hybridization microarrays, gel electrophoretic mobility affects DNA length separations in microchannels, and DNA behavior upon confinement affects nanofluidic devices for DNA separation and manipulation.

[Return to Table of Contents]