Research of DNA stretching on lipid bilayer
Date Issued
2010
Date
2010
Author(s)
Huang, Szu-Chi
Abstract
This thesis focuses on the development of a new platform that is capable of stretching DNA to a high degree while can be manufactured economically. Among current technologies for DNA stretching, confining DNA molecule in a nanochannel has been shown to provide the best stretching uniformity. “Confining DNA” means restricting DNA in a small space. Due to the excluded volume effects, DNA will extend more when the space becomes narrower. However, a reasonable DNA extension can only be achieved when the dimension of a nanochannel reduces to below 100nm, making such nanochannel expensive and difficult to produce. Inspired by the concept of confinement, we develop an alternative approach, called strip confinement, to stretch DNA molecule.
The core concept of strip confinement is to restrict DNA in a strip-shaped two-dimensional plane. The two-dimensional nature of the platform enhances the excluded volume effects, and therefore is more advantageous for the application of DNA stretching. Since DNA is negatively charged in physiological condition, the proposed platform is realized by creating parallel strips of positively charged lipid bilayer on a glass. The processes for manufacturing our platforms, including the creation of the patterned surface and the setup of lipid bilayer, are more economical than those for producing nanochannels. Based on our new approach, we investigate two different ways to stretch DNA, sidewall confinement and direct strip confinement. The former stretches DNA along its corner where the lipid density is highest, the latter stretches DNA along its axis.
The average degree of DNA extension measured from a sidewall confinement is 0.56, close to that obtained from nanochannels with the width between 60nm to 80nm. The degree of DNA extension measured from a Direct strip confinement with 300nm in width is 0.4, a little lower than that of the former method. The results presented here are for proof-of-principle, and we expect that our devices based on the concept of strip confinement can be further improved for better performance and lower cost.
Subjects
Stretch DNA molecule
lipid bilayer
strip confinement
Type
thesis
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