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Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly


Evans, Constantine Glen (2014) Crystals that Count! Physical Principles and Experimental Investigations of DNA Tile Self-Assembly. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/7FMK-9403.


Algorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications.

In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly. We survey recent progress in experimental algorithmic self-assembly, and explain the simple physical models behind this progress. Using direct observation of individual tile attachments and detachments with an atomic force microscope, we test some of the fundamental assumptions of the widely-used kinetic Tile Assembly Model, obtaining results that fit the model to within error. We then depart from the simplest form of that model, examining the effects of DNA sticky end sequence energetics on tile system behavior. We develop theoretical models, sequence assignment algorithms, and a software package, StickyDesign, for sticky end sequence design.

As a demonstration of a specific tile system, we design a binary counting ribbon that can accurately count from a programmable starting value and stop growing after overflowing, resulting in a single system that can construct ribbons of precise and programmable length. In the process of designing the system, we explain numerous considerations that provide insight into more general tile system design, particularly with regards to tile concentrations, facet nucleation, the construction of finite assemblies, and design beyond the abstract Tile Assembly Model.

Finally, we present our crystals that count: experimental results with our binary counting system that represent a significant improvement in the accuracy of experimental algorithmic self-assembly, including crystals that count perfectly with 5 bits from 0 to 31. We show some preliminary experimental results on the construction of our capping system to stop growth after counters overflow, and offer some speculation on potential future directions of the field.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:DNA computing; tile self-assembly; DNA tiles; molecular programming; algorithmic self-assembly; self-assembly; DNA nanotechnology; nanotechnology; biophysics; physics
Degree Grantor:California Institute of Technology
Division:Physics, Mathematics and Astronomy
Major Option:Physics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Winfree, Erik
Thesis Committee:
  • Winfree, Erik (chair)
  • Libbrecht, Kenneth George
  • Rothemund, Paul W. K.
  • Bruck, Jehoshua
  • Pierce, Niles A.
Defense Date:27 May 2014
Record Number:CaltechTHESIS:05132014-142306756
Persistent URL:
Evans, Constantine Glen0000-0002-7053-1670
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8232
Deposited By: Constantine Evans
Deposited On:03 Jun 2014 19:21
Last Modified:04 Oct 2019 00:04

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