Dissertation/Thesis Abstract

Programmable molecular choreography in a DNA transducer produced by self-assembly
by Li, Yuhang, Ph.D., New York University, 2014, 219; 3635349
Abstract (Summary)

Deoxyribonucleic acid (DNA) molecules have been used to create a large variety of complex target structures and functional devices with precisely controlled nanoscale features. In DNA nanotechnology, nucleic acids are more than just the carriers of genetic information, they are excellent engineering materials and structural building blocks with predictable and programmable properties for nanostructures, as they self-assemble following the strict Watson-Crick base pairing rules. DNA nanotechnology can be applied to the field of biomolecular computing by incorporating computation into the assembly of DNA arrays. This algorithmic self-assembly is one of the many ways to build a computing device based on DNA.

In this dissertation, I describe the design and construction of a programmable DNA transducer, which performs divisions in the binary system with the divisor 3. In order to achieve the algorithmic self-assembly, multiple pairs of doubly cohesive sticky ends are designed to simulate different input and output symbols, as well as different remainders of the division. Double cohesion also increases the stability of the system. The answer to the division is represented by an array of double crossover (DX) DNA triangles, either pointing upward or downward on every bit, which can be deciphered as a binary number.

A pair of reciprocal nanomechanical devices are assigned to different outputs, making the different output DX triangles have different orientations. These devices can operate oppositely and synchronously with the same control strands in the same environment, thereby reversing all the output digits at once, and creating a new expression of the original answer. The reciprocal nanomechanical devices work in conjunction with the designed algorithmic self-assembly, and together they co-direct the molecular choreography of the DNA transducer. The correct assemblies of various programmable DNA transducers as well as their molecular choreography performances are verified by atomic force microscopy (AFM). The self-assembled DNA transducer has dimensions large enough to be observed by AFM with a good resolution on every single digit, both input and output, which is a challenge in both design and assembly. Insofar as we are aware, this system is the largest non-periodic and non-origami-based two-dimensional DNA transducing device that has been built.

Indexing (document details)
Advisor: Seeman, Nadrian C.
Commitee: Arora, Paramjit, Broyde, Suse, Canary, James, Vologodskii, Alexander
School: New York University
Department: Chemistry
School Location: United States -- New York
Source: DAI-B 76/01(E), Dissertation Abstracts International
Subjects: Biochemistry, Nanoscience
Keywords: Atomic force microscopy, DNA computing, Molecular choreography, Nanomechanical devices, Self-assembly
Publication Number: 3635349
ISBN: 978-1-321-16343-8
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