Thesis
DNAjig: a new automated design methodology for constructing arbitrary DNA nanostructures
Washington State University
Master of Science (MS), Washington State University
2010
Handle:
https://hdl.handle.net/2376/102330
Abstract
DNA self-assembly is an emerging technique in DNA nanotechnology that holds promise for high impact applications such as in the synthesis of DNA-based nanodevices in medicine, robotics and electronics. Recent advancements in technologies and ideas have spurred new development and a renewed interest in the area. The most significant challenge faced by designers in the field is lack of algorithmic and software options to aid in the design process, and as a result the scope of synthesis has been restricted to modeling a limited set of shapes in 2D. In this thesis, we propose a new design methodology called DNAjig to build DNA nanostructures. The highlights of this method are as follows: i) The construction procedure is based on a novel application of space-filling curves to model the shape of an arbitrary used-specified 2D or 3D object. ii) The method results in a simple, yet recursively constructable design layout that is inherently interlocked iii) Almost all steps within the proposed design procedure can be automated and we present algorithms and a base-version implementation for the same. Along with a new design methodology, we also present new algorithms to select experimentally suitable, non-repetitive regions of a template DNA and a standalone implementation that includes a GUI that is user-friendly and interactive for in silico design of DNA nanostructures. Wetlab validation showing the results of self-assembly of our first batch of computer generated 2D models is presented.
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Details
- Title
- DNAjig
- Creators
- Md. Muksitul Haque
- Contributors
- Ananth Kalyanaraman (Degree Supervisor)
- Awarding Institution
- Washington State University
- Academic Unit
- Electrical Engineering and Computer Science, School of
- Theses and Dissertations
- Master of Science (MS), Washington State University
- Publisher
- Washington State University; Pullman, Wash. :
- Identifiers
- 99900525018301842
- Language
- English
- Resource Type
- Thesis