When William Reville started work at UCC in 1975, the only computer in college was a mainframe machine that filled a large room. Today, almost everyone in college has a personal computer (PC) on their desk that is more powerful than that original mainframe machine.
The name of the game in the computer world is to pack ever more power and speed into smaller and smaller machines. However, development is bound to hit a wall eventually, when the silicon microprocessors on which computers are based reach their limit of speed and miniaturisation. A new material will be needed to make further advances, and some people believe this material is DNA.
The chemical nature of the genetic material in living organisms is deoxyribonucleic acid (DNA). The basic information essential for life is stored in DNA molecules. The information is encoded as linear sequences of four different chemicals, called bases, denoted by the letter symbols A, T, G, C.
The DNA molecule consists of two strands, each bearing a linear sequence of bases, wrapped around each other in a double helix. The bases on each strand bond with the bases on the other strand in a special way. A always pairs with T, G always pairs with C. The two strands are complementary, and if you know the sequence of bases on either strand, you automatically know the sequence on the other strand.
Leonard Adleman, a US computer scientist who concluded that DNA had computational potential after reading The Molecular Biology of the Gene by James Watson, first developed the DNA computer concept. In 1994, Adleman outlined how to use DNA to solve the mathematical Hamilton Path Problem, also known as "The Travelling Salesman Problem" and named after William Rowan Hamilton, who was a famous 19th-century Irish mathematician.
The problem concerns a salesman who wishes to visit many cities, some of which are connected by non-stop flights, starting from one particular city and ending in another particular city and passing through each of the other cities just once - the Hamilton Path. When the cities number around 100 it could take a conventional computer hundreds of years to find the Hamilton Path.
Adleman used DNA to solve a seven-city, 14-flight path problem. This simple case can be solved using pencil and paper in a few minutes, but the DNA solution demonstrated the feasibility of Adleman's proposed DNA computer. He assigned each city its own unique DNA sequence, e.g. ACTTGCAG, that can be visualised as a first name (ACTT) and a second name (GCAG). He assigned each flight number a DNA sequence made up of the last name of the city of origin and the first name of the city of destination.
He chemically synthesised the complementary sequences of the cities and mixed them with the synthesised flight number sequences in a test tube. The test tube contained a fantastic number, 1018 (10 multiplied by itself 18 times), of DNA pieces. They instantly combined by complementary base pairing, with flight numbers linking their respective cities of origins and destinations. All possible pathways between the cities were created, including the Hamilton Path.
Adleman then used a number of relatively laborious chemical procedures to eliminate all the molecules in the mixture that bore wrong answers (he knew how long the DNA encoding the answer must be, he knew the beginning and end city codes, and so on), leaving only the flight paths that began and ended at the correct cities and connected the five other cities in between.
Half a kilo of DNA could store more information than all the electronic computers ever built. Also, the computing power of a water droplet-sized DNA computer could exceed that of the world's most powerful electronic super-computer. More than 10 trillion DNA molecules could hold 10 terabytes of data and perform 10 trillion calculations at the same time.
CONVENTIONAL computers carry out linear calculations (i.e. take on tasks one at a time). Parallel DNA computing power, however, could solve in hours complex mathematical problems which would take electronic computers hundreds of years. The DNA computer is at the very earliest stages of development, but there are several areas currently in active use (or under advanced development).
The National Microelectronics Research Centre at UCC has a number of advanced research projects in these areas. One, in the area of nanobiotechnology, marries breakthroughs in information and communications technology with the information coding capacity of DNA, creating ultrasensitive tools to diagnose disease and for a variety of uses in molecular biology.
William Reville is associate professor in biochemistry and director of microscopy at UCC