We are upgrading the repository! A content freeze is in effect until November 22nd, 2024 - no new submissions will be accepted; however, all content already published will remain publicly available. Please reach out to repository@u.library.arizona.edu with your questions, or if you are a UA affiliate who needs to make content available soon. Note that any new user accounts created after September 22, 2024 will need to be recreated by the user in November after our migration is completed.
Study of stochastic processes and RNA elasticity using optical tweezers
Author
Seol, YeonneIssue Date
2004Keywords
Biophysics, General.Advisor
Visscher, Koen
Metadata
Show full item recordPublisher
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.Abstract
Our main research project is to develop an experimental system to understand the ribosomes as molecular motors. For this purpose, we designed and developed the single molecule ribosome motility assay. In this thesis, we discuss the related steps which we have taken to develop this assay: the instrumentation and four experiments. In the introduction, we illustrate the current experimental scheme and show the preliminary data of the single molecule ribosome translation. In the first two chapters, we discuss two interesting experiments dealing with stochastic problems. In the first chapter, we introduce the idea that the noise can be reduced in certain conditions. We show that the noise can be really reduced but only if added fluctuations have to drive the input into states with reduced intrinsic noise. In the second chapter, we investigate two-state processes experimentally using a simple physical system in which a microscopic bead is trapped in a double-well potential. We discuss how we can control the characteristics of the escape process by adding a periodic force and illustrate the characteristics in terms of the residence time distribution and the escape phase. As last two chapters, we discuss the elastic and structural properties of homopolymeric RNA, polyadenylic acids (poly(A)), polycytidylic acids (poly(C)), and polyuridylic acids (poly(U)). First, we investigate the elastic property of poly(U) as a random coil. We find that the force-extension data is well predicted by a classic worm-like chain model at high Na⁺ concentrations, whereas at low such concentrations the introduction of a scale-dependent persistence length is required. As single-stranded helices, poly(A) and poly(C) are studied. We stretch the molecules to induce the conformational transition from folded states to unfolded states and use the elastically coupled two-state model to acquire their structural information (about 9 bases per turn and 8 bases per turn, for poly(A) and poly(C) respectively, at neutral pH and 500 mM [Na⁺]) and the free energy differences between two states (20 pN·nm for poly(A) and 17.5 pN·nm for poly(C)).Type
textDissertation-Reproduction (electronic)
Degree Name
Ph.D.Degree Level
doctoralDegree Program
Graduate CollegePhysics