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The Self-Replication and Evolution of DNA Crystals

Citation

Schulman, Rebecca (2007) The Self-Replication and Evolution of DNA Crystals. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechETD:etd-04302007-164103

Abstract

How life began is still a mystery. While various theories suggest that life began in deep sea volcanic vents or that a world where life consisted predominantly of RNA molecules preceded us, there is no hard evidence to give shape to the chain of events that led to cellular life.

Perhaps the fundamental enigma of our origins is how life began to self-replicate in such a way that evolution could produce Earth's "endless forms most beautiful." With the exception of biological organisms, we have no examples of self-replicating, evolving chemical systems, despite an extensive research program with the goal of identifying them.

In this thesis, I construct a chemical system that is capable of the most basic self-replication and evolution. The system uses no enzymes or biological sequences, can support and replicate a combinatorial genome, and is completely autonomous. There are no fundamental obstacles to the replication by this system of much more complex sequences or to open-ended evolution.

The design of the system is inspired by the work of Graham Cairns-Smith, who has proposed that life began with clay. Clays are tiny layered crystals; some clay crystals can contain one of several different patterns of atoms or molecules in each layer. The choice of patterns for the layers could be viewed as a sort of genome: it would be copied as the clay grew, and if the crystal broke, each new piece would inherit its pattern from the old piece and could replicate it in the same manner. If some patterns of layers could grow and reproduce faster than other patterns, crystals with faster-growing patterns would be selected for.

Instead of the atoms or small molecules of which clay consists, I use molecules consisting of 4-6 interwoven, synthetic DNA strands called DNA tiles to construct crystals that replicate and evolve as Cairns-Smith imagined. While the choice of construction material was influenced by ease of use -- in contrast to clay crystals, DNA tile crystals have been previously characterized and are easy to crystallize and image in the laboratory -- the choice was fundamentally made because DNA tile monomers are programmable, allowing us to create novel crystal morphologies rationally.

The crystals I construct, termed "zig-zag ribbons", contain a sequence of information ("a genome") in each row. Growth of the ribbon adds rows, one at time, each of which contain an arrangement of DNA tiles that encode the same information sequence as the previous row. Altering the set of tiles used to assemble ribbons allows us to alter the alphabets for and the permitted lengths of sequences that can be copied.

I describe how to design tile sets that can replicate genomes with different alphabets and the kind of sequence evolution that is in theory possible with some simple tile sets. Altering the tile set can not only change the kinds of sequences that may be replicated, it can also make growth and splitting more robust. I show how to make changes to the crystals' design to prevent errors during growth and splitting and to reduce the rate of spontaneous generation of new crystals.

It has been previously shown that DNA tile crystallization can be used to perform universal computation; I show that in theory crystals that can compute can undergo open-ended evolution as they try to produce more and more complex programs to take advantage of available growth resources. This mechanism is simple enough to potentially observe in the laboratory in the near future. In experiments, I demonstrate a much more basic kind of replication and evolution, in which zig-zag ribbons maintain a preference for a certain width into a second generation.

This work suggests that the concept of a self-replicating chemistry is closely related to the concept of a chemistry that can store information and compute. It is only by clearly understanding how chemistry can perform these latter tasks that we can hope to understand how self-replication and evolution can occur, and by implication, understand how life might have begun.





Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:cellular automata; chemical computation; DNA nanotechnology; evolution; origin of life; self-assembly; self-replication
Degree Grantor:California Institute of Technology
Division:Engineering and Applied Science
Major Option:Computation and Neural Systems
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Winfree, Erik
Thesis Committee:
  • Abu-Mostafa, Yaser S. (chair)
  • Yurke, Bernard
  • Winfree, Erik
  • Joyce, Gerald
  • Bruck, Jehoshua
  • Wang, Zhen-Gang
Defense Date:11 May 2007
Record Number:CaltechETD:etd-04302007-164103
Persistent URL:http://resolver.caltech.edu/CaltechETD:etd-04302007-164103
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1554
Collection:CaltechTHESIS
Deposited By: Imported from ETD-db
Deposited On:30 May 2007
Last Modified:26 Dec 2012 02:39

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