DNA Computing - Foundations and Implications

DNA computing is an area of natural computing based on the idea that molecular biology processes can be used to perform arithmetic and logic operations on information encoded as DNA strands. The aim of this review is two-fold. First, we introduce the fundamentals of DNA computing, including basics of DNA structure and bio-operations, and two historically important DNA computing experiments. Secondly, we describe some of the ways in which DNA computing research has impacted fields in theoretical computer science. The first part of this review outlines basic molecular biology notions necessary for understanding DNA computing (Section 2), recounts the first experimental demonstration of DNA computing (Section 3), as well as the milestone wet laboratory experiment that first demonstrated the potential of DNA computing to outperform the computational ability of an unaided human (Section 4). The second part of the review describes how the properties of DNA-based information, and in particular the Watson-Crick complementarity of DNA single strands, have influenced areas of theoretical computer science such as formal language theory, coding theory, automata theory and combinatorics on words. More precisely, Section 5 summarizes notions and results in formal language theory and coding theory arising from the problem of design of optimal encodings for DNA computing experiments: Section 5.1 describes the problem of DNA encodings design, Section 5.2 consists of an analysis of intramolecular bonds (bonds within a given DNA strand), Section 5.3 defines and characterizes languages that avoid certain undesirable intermolecular bonds (bonds between two or more DNA strands), and Section 5.4 investigates languages whose words avoid even imperfect bindings between their constituent strands. Section 6 contains another, vectorial, representation of DNA strands and two computational models based on this representation: sticker systems and Watson-Crick automata. After a brief description of the representation of DNA partial double strands as two-line vectors, and of the sticking operation that combines them, Section 6.1 describes basic sticker systems, sticker systems