Studies of DNA dynamics in slit-like nanochannel confinement

The ability to visually observe single DNA molecules has greatly improved our understanding of polymer physics, from gel electrophoresis to the theology of dilute (and even concentrated) polymer solutions. The use of DNA in these general studies, though, resulted in a depth of specific knowledge concerning a particular polymer of major interest in biology. Researchers have taken advantage of this wealth of knowledge to develop new, faster, cheaper, and more direct methods of extracting the information, at a coarse level, embedded in the sequence of basepairs along the DNA backbone. Further development, though, is now limited by the ability to control and manipulate the position and conformation of single DNA molecules. It was recognized long ago that confinement of polymer molecules in geometries with dimensions on the order of the polymer size would greatly affect the physical behavior of that polymer. These physical changes were later hypothesized to be of use to control single molecules of DNA. However, until recently, the confinement theories and their use stood untested due to a lack of techniques to reliably and controllably construct micro- (and nano-) devices with such small feature sizes. It is the focus of this thesis to investigate these confinement effects in an ideal, nanofabricated geometry and their use in the manipulation and control of single DNA molecules. In this thesis, we present a series of single-molecule visualization studies aimed at elucidating polymer behavior in confinement and methods of possible use in the manipulation and control of the polymer conformation. In particular, confinement in a slit was shown, both experimentally and through scaling analysis, to diminish long length scale polymer-induced solvent flow sufficiently enough to render those effects negligible in the behavior of the confined molecule. We also demonstrate that confinement also alters the diffusion and relaxation time of the DNA, and we compare their dependence on channel height and molecular weight to existing theories.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemical Engineering.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2008

Author dc:creator

• Balducci, Anthony (Anthony G.)

Advisor dc:contributor.advisor

• Patrick S. Doyle.

• Chemical Engineering.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/45916

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/45916