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MOTIONS AND CONFORMATIONS OF NUCLEIC ACIDS STUDIED USING
SITE-DIRECTED SPIN LABELING
by
Gian Paola Gacho Grant
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Reguirements for the Degree
DOCTOR OF PHILOSOPHY
(CHEMISTRY)
December 2009
Copyright 2009 Gian Paola Gacho Grant
Object Description
| Title | Motions and conformations of nucleic acids studied using site-directed spin labeling |
| Author | Grant, Gian Paola Gacho |
| Author email | gacho@usc.edu; gian37@yahoo.com |
| Degree | Doctor of Philosophy |
| Document type | Dissertation |
| Degree program | Chemistry |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2009-07-01 |
| Date submitted | 2009 |
| Restricted until | Unrestricted |
| Date published | 2009-09-03 |
| Advisor (committee chair) | Qin, Peter Z. |
| Advisor (committee member) |
Chen, Lin Haworth, Ian S. |
| Abstract | Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) play crucial roles in life. They carry and transmit genetic information, regulate and maintain gene expression, and in certain cases, catalyze biochemical reactions. In order to achieve these various functions, nucleic acids adopt complex and dynamic three-dimensional structures. The focus of this dissertation is to develop and apply the site-directed spin labeling (SDSL) method to study motions and conformations in nucleic acids. On the strategy of SDSL, the first step is to attach the spin label to the macromolecule. Research here provides a new approach of attaching nitroxides at the 5’ terminus of nucleic acids using enzymatic reaction. A method was also developed to characterize and separate diasteromeric nitroxide-labeled nucleic acids formed from spin labeling via the modified backbone position. On the application of SDSL, research here successfully obtained two types of structural information in nucleic acids. First, specific duplex motions within a large RNA were investigated using CW-EPR experiments. These motions are critical for the catalytic activity of the group I ribozyme. Second, distances were measured at specific positions of adenosine-tract rich DNA using double double electron resonance spectroscopy (DEER). Distances measured are used to determine the sensitivity of DEER method in probing conformational variation across A-tract containing double-stranded DNAs. Studies here advanced the utility of site-directed spin labeling to obtain structure and motional information in nucleic acids where other technologies have difficulty. This is a step in unraveling the relationship of structure, dynamics, and function in DNA and RNA. |
| Keyword | site-directed spin labeling; DNA; RNA; structure; dynamics; EPR |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m2583 |
| Contributing entity | University of Southern California |
| Rights | Grant, Gian Paola Gacho |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | cisadmin@dots.usc.edu |
| Filename | etd-Grant-2177 |
| Archival file | uscthesesreloadpub_Volume32/etd-Grant-2177.pdf |
Description
| Title | Page 1 |
| Contributing entity | University of Southern California |
| Repository email | cisadmin@dots.usc.edu |
| Full text | MOTIONS AND CONFORMATIONS OF NUCLEIC ACIDS STUDIED USING SITE-DIRECTED SPIN LABELING by Gian Paola Gacho Grant A Dissertation Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Reguirements for the Degree DOCTOR OF PHILOSOPHY (CHEMISTRY) December 2009 Copyright 2009 Gian Paola Gacho Grant |
