Single stranded DNA: A new model system for single molecule polymer dynamics
Brockman, Christopher A.
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https://hdl.handle.net/2142/24412
Description
Title
Single stranded DNA: A new model system for single molecule polymer dynamics
Author(s)
Brockman, Christopher A.
Issue Date
2011-05-25T14:40:33Z
Director of Research (if dissertation) or Advisor (if thesis)
Schroeder, Charles M.
Department of Study
Chemical & Biomolecular Engr
Discipline
Chemical Engineering
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Keyword(s)
single molecule
polymer dynamics
rolling circle replication
fluorescence microscopy
Abstract
The study of polymer dynamics has been an active area of research for many years. For nearly two decades, fluorescently-labeled double stranded DNA (dsDNA) has been the model system for studying single molecule polymer dynamics in non-equilibrium conditions. However, dsDNA is a semiflexible polymer with markedly different local molecular properties compared to flexible polymer chains, such as synthetic organic polymers. In this work, we developed a new model system for single molecule studies of flexible polymers based on single stranded DNA (ssDNA). Using a biochemical synthesis scheme called rolling circle replication, long strands (>25 µm) of ssDNA containing “designer sequences” have been generated to prevent intramolecular base pairing. Polymer chains are synthesized with amine modified bases incorporated along the backbone to facilitate labeling with fluorescent dyes. As proof-of-principle demonstration of this new chemical platform, we use epifluorescence microscopy to image individual ssDNA molecules stretching in an extensional flow generated inside a microfluidic device. It is anticipated that the model polymer system presented here will serve to promote further investigations of flexible polymer dynamics at the molecular level.
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