DNA (Deoxyribose Nucleic Acid) computing, also known as molecular computing is a new approach to massively parallel computation based on groundbreaking work by Adleman. DNA computing was proposed as a means of solving a class of intractable computational problems in which the computing time can grow exponentially with problem size (the 'NP- complete' or non-deterministic polynomial time complete problems).

A DNA computer is basically a collection of specially selected DNA strands whose combinations will result in the solution to some problem, depending on the problem at hand. Technology is currently available both to select the initial strands and to filter the final solution. DNA computing is a new computational paradigm that employs (bio)molecular manipulation to solve computational problems, at the same time exploring natural processes as computational models. In 1994, Leonard Adleman at the Laboratory of Molecular Science, Department of Computer Science, University of Southern California surprised the scientific community by using the tools of molecular biology to solve a different computational problem.

The main idea was the encoding of data in DNA strands and the use of tools from molecular biology to execute computational operations. Besides the novelty of this approach, molecular computing has the potential to outperform electronic computers.

For example, DNA computations may use a billion times less energy than an electronic computer while storing data in a trillion times less space. Moreover, computing with DNA is highly parallel: In principle there could be billions upon trillions of DNA molecules undergoing chemical reactions, that is, performing computations, simultaneously.

Principles of DNA Computing

DNA is the major information storage molecule in living cells, and billions of years of evolution have tested and refined both this wonderful informational molecule and highly specific enzymes that can either duplicate the information in DNA molecules or transmit this information to other DNA molecules. Instead of using electrical impulses to represent bits of information, the DNA computer uses the chemical properties of these molecules by examining the patterns of combination or growth of the molecules or strings. DNA can do this through the manufacture of enzymes, which are biological catalysts that could be called the ’software’, used to execute the desired calculation.

A single strand of DNA is similar to a string consisting of a combination of four different symbols A G C T. Mathematically this means we have at our disposal a letter alphabet, Σ = {A GC T} to encode information which is more than enough considering that an electronic computer needs only two digits and for the same purpose. In a DNA computer, computation takes place in test tubes or on a glass slide coated in 24K gold. The input and output are both strands of DNA, whose genetic sequences encode certain information. A program on a DNA computer is executed as a series of biochemical operations, which have the effect of synthesizing, extracting, modifying and cloning the DNA strands.