Optical Tweezers studies of Nucleic Acids and their Interaction with Proteins
Item Type text; Electronic Dissertation
Authors Kalafut, Bennett Samuel
Publisher The University of Arizona.
Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Download date 04/10/2021 02:42:51
Link to Item http://hdl.handle.net/10150/202969 OPTICAL TWEEZERS STUDIES OF NUCLEIC ACIDS AND THEIR INTERACTION WITH PROTEINS
by
Bennett Samuel Kalafut
Copyright © Bennett Samuel Kalafut 2011
A Dissertation Submitted to the Faculty of the
DEPARTMENT OF PHYSICS
In Partial Fulfillment of the Requirements For the Degree of
DOCTOR OF PHILOSOPHY
In the Graduate College
THE UNIVERSITY OF ARIZONA
2011 2
THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE
As members of the Dissertation Committee, we certify that we have read the dis- sertation prepared by Bennett Samuel Kalafut entitled Optical Tweezers studies of Nucleic Acids and their Interaction with Pro- teins and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy.
Date: 20 September 2011 Koen Visscher
Date: 20 September 2011 William Bickel
Date: 20 September 2011 Michael Brown
Date: 20 September 2011 Srinivas Manne
Date: 20 September 2011 Joseph Watkins
Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my direction and recommend that it be accepted as fulfilling the dissertation requirement.
Date: 20 September 2011 Dissertation Director: Koen Visscher 3
STATEMENT BY AUTHOR
This dissertation has been submitted in partial fulfillment of requirements for an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library.
Brief quotations from this dissertation are allowable without special permission, provided that accurate acknowledgment of source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the copyright holder.
SIGNED: Bennett Samuel Kalafut 4
ACKNOWLEDGEMENTS
Many people deserve credit for their contribution to this work, including five I single out below: It would be difficult to overstate the thanks owed to Gary M. Skinner. The T7 RNA Polymerase assay reported in Chapter 2 was brought with him from the University of York to the University of Arizona [1, 2], and in that investigation he did the great majority of the difficult experimental work. Gary also had the patience to teach this physicist practical wet-lab technique and a considerable amount of biology. The experiments on RNA homopolymers presented in Chapter 3 build on an intellectual foundation laid by Yeonee Seol [3], who also was the major builder and programmer of the instrument on which, with some refinements, the reported RNA-stretching measurements were taken. When I was searching for a way to analyze problematic single-molecule fluores- cence data, it was a pointer from Joseph Watkins to the changepoint literature that started me on the path to develop the algorithm presented in Chapter 4. Joe has also been a very reliable source of advice on statistics during my time as a doctoral student, and is the originator of the intersection-of-curves method of estimation presented in Section 2.5. Rae Ana Snyder (Kalafut) was among the first to receive even qualitative re- ports of the RNA stretching results presented in Figures 3.4 and 3.7, including the then-enigmatic difference in transi