The combination of different recognition/instruction features in a molecular program opens a door to the design of self-organizing systems capable of performing molecular computation. Recent studies described the use of biomolecules and DNA-based protocols to solve computational problems. An approach making use of specifically designed nonnatural components could provide higher diversity, better resistance to fatigue, and smaller size.
Computation with biomolecules Junghuei Chen and David Harlan Wood (PNAS Vol. 97, Issue 4, 1328-1330, February 15, 2000)
Molecular computation: RNA solutions to chess problems Dirk Faulhammer*, Anthony R. Cukras*, Richard J. Lipton, and Laura F. Landweber (PNAS Vol. 97, Issue 4, 1385-1389, February 15, 2000)
Deoxyribozyme-Based Logic Gates Milan N. Stojanovic,* Tiffany Elizabeth Mitchell, and Darko Stefanovic (J. Am. Chem. Soc., 124 (14), 3555 -3561, 2002)
We report herein a set of deoxyribozyme-based logic gates capable of generating any Boolean function. We construct basic NOT and AND gates, followed by the more complex XOR gate. These gates were constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxyribozymes. Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in solution. The operation of these gates is conveniently connected to a fluorescent readout.
Journal of Computational Biology ...for example:
On Combinatorial DNA Word Design Author(s): Amit Marathe; Anne E. Condon; Robert M. Corn
Source: Journal of Computational Biology
Volume: 8 Number: 3 Page: 201 -- 219Abstract: We consider the problem of designing DNA codes, namely sets of equi-length words over the alphabet {A, C, G, T} that satisfy certain combinatorial constraints. This problem is motivated by the task of reliably storing and retrieving information in synthetic DNA strands for use in DNA computing or as molecular bar codes in chemical libraries. The primary constraints that we consider, defined with respect to a parameter d, are as follows: for every pair of words w, x in a code, there are at least d mismatches between w and x if w x and also between the reverse of w and the Watson-Crick complement of x. Extending classical results from coding theory, we present several upper and lower bounds on the maximum size of such DNA codes and give methods for constructing such codes. An additional constraint that is relevant to the design of DNA codes is that the free energies and enthalpies of the code words, and thus the melting temperatures, be similar. We describe dynamic programming algorithms that can (a) calculate the total number of words of length n whose free energy value, as approximated by a formula of Breslauer et al. (1986) falls in a given range, and (b) output a random such word. These algorithms are intended for use in heuristic algorithms for constructing DNA codes.
and
Title: Fidelity of Enzymatic Ligation for DNA Computing
Author(s): Dirk Faulhammer; Richard J. Lipton; Laura F. Landweber
Source: Journal of Computational Biology Volume: 7 Number: 6 Page: 839 -- 848Abstract: We describe a convenient assay for rapid qualitative evaluation of hybridization/ligation fidelity. The approach uses randomized probe strands of DNA and restriction enzyme digestion after amplification of reaction products by the polymerase chain reaction (PCR). We report ligation efficiencies and fidelities of two DNA ligases, T4 DNA ligase and Thermus aquaticus (Taq) DNA ligase, over a range of temperatures.
Here's one that cites Lipton 1995:
Programmable and autonomous computing machine made of biomolecules
Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E
NATURE 414 (6862): 430-434 NOV 22 2001Abstract: Devices that convert information from one form into another according to a definite procedure are known as automata. One such hypothetical device is the universal Turing machine(1), which stimulated work leading to the development of modern computers. The Turing machine and its special cases(2), including finite automata(3), operate by scanning a data tape, whose striking analogy to information-encoding biopolymers inspired several designs for molecular DNA computers(4-8). Laboratory-scale computing using DNA and human-assisted protocols has been demonstrated(9-15), but the realization of computing devices operating autonomously on the molecular scale remains rare(16-20). Here we describe a programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously. The automaton's hardware consists of a restriction nuclease and ligase, the software and input are encoded by double-stranded DNA, and programming amounts to choosing appropriate software molecules. Upon mixing solutions containing these components, the automaton processes the input molecule via a cascade of restriction, hybridization and ligation cycles, producing a detectable output molecule that encodes the automaton's final state, and thus the computational result. In our implementation 10(12) automata sharing the same software run independently and in parallel on inputs (which could, in principle, be distinct) in 120 mul solution at room temperature at a combined rate of 10(9) transitions per second with a transition fidelity greater than 99.8%, consuming less than 10(-10) W.