DNA Computation: Theory, Practice, and Prospects

Abstract

L. M. Adleman launched the field of DNA computing with a demonstration in 1994 that strands of DNA could be used to solve the Hamiltonian path problem for a simple graph. He also identified three broad categories of open questions for the field. First, is DNA capable of universal computation? Second, what kinds of algorithms can DNA implement? Third, can the error rates in the manipulations of the DNA be controlled enough to allow for useful computation? In the two years that have followed, theoretical work has shown that DNA is in fact capable of universal computation. Furthermore, algorithms for solving interesting questions, like breaking the Data Encryption Standard, have been described using currently available technology and methods. Finally, a few algorithms have been proposed to handle some of the apparently crippling error rates in a few of the common processes used to manipulate DNA. It is thus unlikely that DNA computation is doomed to be only a passing curiosity. However, much work remains to be done on the containment and correction of errors. It is far from clear if the problems in the error rates can be solved sufficiently to ever allow for general-purpose computation that will challenge the more popular substrates for computation. Unfortunately, biological demonstrations of the theoretical results have been sadly lacking. To date, only the simplest of computations have been carried out in DNA. To make significant progress, the field will require both the assessment of the practicality of the different manipulations of DNA and the implementation of algorithms for realistic problems. Theoreticians, in collaboration with experimentalists, can contribute to this research program by settling on a small set of practical and efficient models for DNA computation.