Theoretical and Experimental DNA Computation (Natural ...

5.11 Bibliographical Notes 145
which direct the assembly of the macrostructure. The tiles then self-assemble
to perform a computation. The authors of [103] report successful XOR computations
on pairs of bits, but note that the scalability of the approach relies on
proper hairpin formation in very long single-stranded molecules, which cannot
be assumed.
We now briefly describe some “late-breaking” results. The construction of
molecular automata (see Chap. 3) was demonstrated by Benenson et al. in [27].
This experiment builds on the authors’ earlier work [28] on the construction
of biomolecular machines. In [27], the authors describe the construction of a
molecular automaton that uses the process of DNA backbone hydrolysis and
strand hybridization, fuelled by the potential free energy stored in the DNA
itself.
Related work, due to Stojanovic and Stefanovic [147], describes a molecular
automaton that plays the game of tic-tac-toe (or noughts and crosses)
against a human opponent. The automaton is a Boolean network of deoxribozymes
incorporating 23 molecular-scale logic gates and one constitutively
active deozyribozyme arrayed in a 3×3 well formation (to represent the game
board). The human player signals a move by adding an input oligo, and the
automaton’s move is signalled by fluorescence in a particular well. This cycle
continues until there is either a draw or a victory for the automaton, as it
plays a perfect strategy and cannot be defeated.
5.10 Summary
In this chapter we have described in depth the experimental realization of
some of the abstract models of DNA computation described in Chap. 2. We
described Adleman’s seminal experiment, as well as a potential implementation
of the parallel filtering model, which laid the foundations for important
later work on destructive algorithms. We also described some key contributions
to the laboratory implementation of computations, and highlighted some
late-breaking results.
5.11 Bibliographical Notes
The use of molecules other than DNA (for example, proteins and chemical
systems) is reviewed and discussed in [144]. Chen and Wood [44] review early
work on implementations of biomolecular computatons, and suggest potentially
useful lines of enquiry. The recent proceedings of the International Workshop
on DNA Based Computers [43, 73] contain many articles on laboratory
implementations, including notable papers on whiplash PCR [105] and DNAbased
memory [42].