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Title:Transport properties of DNA nanostructures
Author(s):Li, Chen-Yu
Director of Research:Aksimentiev, Aleksei
Doctoral Committee Chair(s):Aksimentiev, Aleksei
Doctoral Committee Member(s):Lu, Yi; Schleife, Andre; Shukla, Diwakar
Department / Program:School of Molecular & Cell Bio
Discipline:Biophysics & Computnl Biology
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):DNA origami, Molecular Dynamics simulation
Abstract:Besides the role of genetic information storage, DNA has been proposed as a new material in nanotechnology. The idea came from the nature-occurring Holliday junction (HJ) which allows more than 2 DNA strands to be assembled. Multiple HJs can be combined with desired orientation to form complex 2- or 3-dimensional objects. One of the most popular methods that realize this concept is the DNA origami. The basic principle of DNA origami is the programmed folding of a long (tens of thousands of nucleotides) DNA strand into a custom shape, guided by multiple specially designed short DNA strands which connect different parts of the long DNA strand through HJs. Since its first demonstration in 2006, not only large (up to hundreds of nanometers) and complex 3D objects with sub-nanometer precision have been produced, but some of them were able to perform active functions. Experimental techniques, including atomic force spectroscopy, small-angle X-ray scattering, transmission electron microscopy (TEM), super-resolution optical imaging, FRET and magnetic tweezers, have been applied to study the global structure and dynamics of the DNA nanostructures. Recently, an atomic-level model of DNA origami in situ has also been obtained, which showed considerable deviation from the idealized structure. A few experimental studies reported the ionic permeability of DNA origami constructs placed on top of a solid-state support or embedded in a lipid bilayer membrane. However, the transport properties of DNA nanostructures and the underlying mechanism have remained relatively unexplored. Here, several simulation studies focusing on the transport properties of DNA nanostructures are pre- sented. Specifically, a comprehensive study on the ionic conductivity and mechanical properties of DNA plates of different lattice type, the number of layers, nucleotide content and cross-over pattern in the electric field were performed. The ionic conductances of a range of DNA channels embedded in lipid membrane were obtained. Several factors were found to affect the ionic conductances of DNA channels, including channel aggregation, channel unfolding and blocking by lipid molecules. The smallest and the largest DNA channels so far were developed. The first DNA scramblase which facilitates the translocation of lipid molecules across the membrane was developed. These works represent potential applications of DNA nanostructures in biosensing, nanofluidics, drug delivery and biomedical engineering.
Issue Date:2017-07-10
Type:Thesis
URI:http://hdl.handle.net/2142/98248
Rights Information:Copyright 2017 Chen-Yu Li.
Date Available in IDEALS:2017-09-29
Date Deposited:2017-08


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