Alexandria Digital Research Library

Single-molecule manipulation measurements of polymer/solution interactions

Author:
Dittmore, Andrew N.
Degree Grantor:
University of California, Santa Barbara. Materials
Degree Supervisor:
Omar A. Saleh
Place of Publication:
[Santa Barbara, Calif.]
Publisher:
University of California, Santa Barbara
Creation Date:
2013
Issued Date:
2013
Topics:
Engineering, Materials Science, Chemistry, Polymer, and Biophysics, General
Keywords:
Protein folding
Polymer
Ionic atmosphere
Chain structure
Excluded volume
Single-molecule
Genres:
Online resources and Dissertations, Academic
Dissertation:
Ph.D.--University of California, Santa Barbara, 2013
Description:

Because the properties of soft materials emerge from the physics of the constituent polymers, we are motivated to characterize chain molecules at a fundamental level. We build upon the magnetic tweezers single-molecule manipulation technique, which involves measuring the distance between the ends of a polymer in real time and with nanometer precision while applying stable magnetic stretching forces in the piconewton range. Here we demonstrate new applications of this technique, specifically by measuring the interactions between a polymer and the surrounding solvent. First, through low-force elastic measurements, we determine a range of fundamental parameters that quantify solvent quality and chain structure. We present a force-solvent phase diagram to summarize these parameters and our experimental data, and discuss where PEG, DNA, RNA, and proteins fit into the diagram. The unstructured and structured states of a biomolecule reside at opposite ends of the diagram, indicating that folding is accompanied by a change in the character of the solvent. We therefore chose to investigate the local solvent change that occurs when a charged biomolecule folds. We present a thermodynamic framework for measuring the uptake of counterions that accompanies nucleic acid folding. Our measurements of a simple DNA hairpin identify potential shortcomings in thermodynamic parameters of MFOLD, the most widely used predictive software for nucleic acids. Finally, we present a variety of polymer immobilization schemes, achieve low-noise measurements with a strong magnet design, identify new assays, and provide technical guidance that may be useful to those interested in pursuing future magnetic tweezers experiments.

Physical Description:
1 online resource (124 pages)
Format:
Text
Collection(s):
UCSB electronic theses and dissertations
ARK:
ark:/48907/f3kw5d1b
ISBN:
9781303538261
Catalog System Number:
990040924340203776
Rights:
Inc.icon only.dark In Copyright
Copyright Holder:
Andrew Dittmore
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