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DNA Technology Beyond Genetics

By Jeremy Lateiner

In 1994, DNA researcher Leonard Adleman made a groundbreaking discovery. Adleman found that he could solve a mathematical problem with DNA. Instead of using silicon, metal and plastic to create a new machine, Adleman used a teaspoon of water, DNA and a test tube. And instead of being fueled by electronics this unconventional computer was fueled by DNA - the chemical blueprint of all life on earth. The information contained on each molecule of DNA is encoded by combinations of four different chemical groups called base pairs. Nature already uses this code like a computer running a random number generator (a major contributing factor to the diversity of life). Adleman discovered he could put nature's tool to his own use.
The first DNA computer was set up to solve a classic mathematical problem: the traveling salesman. This problem uses the scenario of a door-to-door peddler who must visit several cities - only some of which connect - without going through any city twice. To solve this problem using DNA, the first step is to assign a genetic sequence to each city. For example, the city of Los Angeles might be coded GCACAGT. If two cities connect, then the connecting genetic sequence is assigned the first three letters of one city and the last three letters of the other. For example, if Los Angeles connected to New York, the first three letters of Los Angeles (GCA) would connect to the last three letters of New York (CGT). When mixed in solution, the rules of DNA base pairing will only allow connected cities to "connect" with each other on the final DNA molecule. To find out which cities connect, Adleman had to purify his final DNA molecule and analyze the base pair sequence. In a three-city example, the correct solution can only be as long as a sequence determined by the three cities plus two connecting sequences. Therefore the answer becomes the remaining stretch of DNA after incorrect sequences have been discarded. Adleman's experiment involved seven cities, however, and the actual city coding sequence was much longer.

At the time of Adleman's original experiment, DNA computers seemed an appealing alternative to the traditional computer platform. It is generally believed that computers can only go so far on silicon and metal. The quest for more speed and power in computers continues despite this belief. With the ever-increasing numbers of individual transistors that must be crammed onto silicon chips, transistors are getting smaller and smaller. Within several decades, these transistors are expected to reach the size of atoms. DNA computing appears to be a way of getting around the limits imposed by silicon and metal. Since each DNA molecule works like an individual computer, a DNA computer could compute an unbelievable number of operations in a single step while consuming almost no energy. This kind of computing power far exceeds even the most powerful supercomputers of today.

Despite its appeal, DNA computers present many practical difficulties. In theory, a small jar can store millions of times as much information as today's largest computer. Skeptics point out that to solve a truly large mathematical problem with a DNA computer, however, oceans of DNA would be required. Others call attention to the large-amounts of expensive enzymes required to set up each DNA computing reaction. Still others argue that the natural "messiness" of DNA's chemical reactions could doom computers that use it to unacceptably high error rates. Even so, the development of DNA as a computing tool continues, and the day may be fast approaching when DNA rivals its silicon counterparts for computing supremacy.

	DNA Technology Beyond Genetics

	By Jeremy Lateiner In 1994, DNA researcher Leonard Adleman made a groundbreaking discovery. Adleman found that he could solve a mathematical problem with DNA. Instead of using silicon, metal and plastic to create a new machine, Adleman used a teaspoon of water, DNA and a test tube. And instead of being fueled by electronics this unconventional computer was fueled by DNA - the chemical blueprint of all life on earth. The information contained on each molecule of DNA is encoded by combinations of four different chemical groups called base pairs. Nature already uses this code like a computer running a random number generator (a major contributing factor to the diversity of life). Adleman discovered he could put nature's tool to his own use. The first DNA computer was set up to solve a classic mathematical problem: the traveling salesman. This problem uses the scenario of a door-to-door peddler who must visit several cities - only some of which connect - without going through any city twice. To solve this problem using DNA, the first step is to assign a genetic sequence to each city. For example, the city of Los Angeles might be coded GCACAGT. If two cities connect, then the connecting genetic sequence is assigned the first three letters of one city and the last three letters of the other. For example, if Los Angeles connected to New York, the first three letters of Los Angeles (GCA) would connect to the last three letters of New York (CGT). When mixed in solution, the rules of DNA base pairing will only allow connected cities to "connect" with each other on the final DNA molecule. To find out which cities connect, Adleman had to purify his final DNA molecule and analyze the base pair sequence. In a three-city example, the correct solution can only be as long as a sequence determined by the three cities plus two connecting sequences. Therefore the answer becomes the remaining stretch of DNA after incorrect sequences have been discarded. Adleman's experiment involved seven cities, however, and the actual city coding sequence was much longer. At the time of Adleman's original experiment, DNA computers seemed an appealing alternative to the traditional computer platform. It is generally believed that computers can only go so far on silicon and metal. The quest for more speed and power in computers continues despite this belief. With the ever-increasing numbers of individual transistors that must be crammed onto silicon chips, transistors are getting smaller and smaller. Within several decades, these transistors are expected to reach the size of atoms. DNA computing appears to be a way of getting around the limits imposed by silicon and metal. Since each DNA molecule works like an individual computer, a DNA computer could compute an unbelievable number of operations in a single step while consuming almost no energy. This kind of computing power far exceeds even the most powerful supercomputers of today. Despite its appeal, DNA computers present many practical difficulties. In theory, a small jar can store millions of times as much information as today's largest computer. Skeptics point out that to solve a truly large mathematical problem with a DNA computer, however, oceans of DNA would be required. Others call attention to the large-amounts of expensive enzymes required to set up each DNA computing reaction. Still others argue that the natural "messiness" of DNA's chemical reactions could doom computers that use it to unacceptably high error rates. Even so, the development of DNA as a computing tool continues, and the day may be fast approaching when DNA rivals its silicon counterparts for computing supremacy.