DNA-based computation

Computing (or information processing) is central to many areas of science, so computer science is interdisciplinary. For example, the scientific interaction between computer science and biology dates back to the beginnings of computer science. Computer scientists cooperated with biologists in modeling biological phenomena, which helped biologists better understand their problems. In fact, computer science has enormous influence in all walks of life—this phenomenon is often called the computer revolution, which is fueled by the enormous and continuous development of computer technology. The computer industry has followed Moore’s law for a long time, but many real-world problems are intrinsically difficult and thus require parallel processing on a massive scale, and the limits of possible miniaturization using silicon technology are lurking on the horizon. In search of resolving these fundamental obstacles, computer scientists have turned to Mother Nature, which has led to the rise of natural computing—computing inspired by nature. Research in natural computing is concerned with the design and theoretical and empirical understanding of computing gleaned from nature. Characteristic to natural computing is the metaphorical use of concepts, principles, and mechanisms underlying natural systems. For example, evolutionary algorithms use the concepts of mutation, recombination, and natural selection in biology, whereas neural networks are inspired by the highly interconnected neural structures in the human brain and nervous system. In both cases, the algorithms are implemented on conventional silicon-based computers. Molecular computing is much bolder: Next to its own novel paradigms, it also aims to implement algorithms based on these paradigms in biological hardware (or bioware) using, for example, DNA molecules and enzymes.1 Although molecular computing is now a flourishing and quickly growing research area, it was science fiction (modern alchemy?) not so long ago. Richard Feynman first proposed the idea of molecular computing in his famous paper, “There’s Plenty of Room at the Bottom,”2 but it took more than 30 years until Leonard Adleman tested computing with molecules in a biological experiment.3 During this time, scientists made tremendous progress in molecular biology, which resulted in the thorough understanding of the structure of DNA molecules and a handy toolbox for processing them. Adleman’s experiment took full advantage of these achievements.