Nanomechanics of Nucleic Acid Structures Investigated with AFM Based Force Spectroscopy

Nanomechanics of Nucleic Acid Structures Investigated with AFM Based Force Spectroscopy by Mahir Rabbi Department of Mechanical Engineering and Materials Science, Duke University December 08, 2010 ________________________________________________________ Piotr Marszalek, Supervisor ________________________________________________________ David Beratan ________________________________________________________ Anne Lazarides _________________________________________________________ Stefan Zauscher An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Mechanical Engineering and Materials Science in the Graduate School of Duke University 2010 Copyright by Mahir Rabbi 2010 iv Abstract Nucleic acids are subjected to many different mechanical loadings. These loadings could cause large deformations and conformational changes to these molecules. This is why the mechanical properties of nucleic acids are so important to their functions. Here we use a newly designed and built high-performance AFM force spectrometer, supplemented with molecular dynamics simulations and NMR spectroscopy to investigate the relationship between mechanical properties and structure of different