Polymers in Confined Geometry.pdf

2 CHAPTER 1. INTRODUCTION
(a) 100 nm channel width (b) 200 nm channel width
Figure 1.1: Scanning electron micrograph (SEM) picture of nanochannels. These channels
are used in experiments to study the behavior of DNA under increasing confinement. Courtesy
of W. Reisner et al. [38].
real time optical microscopy on fluorescently dyed polymers a direct observation
method of polymer chains has become available.
One important task is the localization of binding sites for restriction and
other DNA binding enzymes. The restriction sites are traditionally determined
by measuring the length of restriction fragments by gel-electrophoresis. Alternatively,
they can be located by using optical mapping of stretched DNA molecules
trapped on a surface. To measure the contour-length of a single molecule using
optical techniques directly, it is necessary to extend the polymer such that
a one-to-one mapping can be established between the spatial position along the
polymer and the position within the genome.
Chip-based devices, that cannot only detect and separate single DNA molecules
by size but are able to sequence at the single molecule level, would have the
potential to revolutionize biology.
Confinement elongation of genomic-length DNA has several advantages over
alternative techniques for extending DNA, such as flow stretching and/or stretching
relying on a tethered molecule. Confinement elongation does not require the
presence of a known external force because a molecule in a nanochannel will remain
stretched in its equilibrium configuration. Second, it allows for a precise
measurement of length at the single molecule level (cf. [44]).
While a number of approaches have been proposed, all of them have in common
the confinement of DNA to nanometer scales, typically 5-200 nm. Confinement
alters the statistical mechanical properties of DNA. A DNA molecule in a
nanochannel (cf. figures 1.1) will extend along the channel axis to a substantial
fraction of its full contour length (cf. figures 1.2). While the study of confined
DNA is interesting from a physical perspective, it is also critical for device design,
potentially leading to new applications of nanoconfinement, for example, the use
of nanochannels to pre-stretch and stabilize DNA before threading through a