DNA Computing

Computers, by definition, are machines which receivesolve a Hamiltonian Path Problem. Their research was
input, manipulate and store the input, and produce anreported in a July 2009 article in the Journal of
output. They've quickly grown in the size andBiological Engineering. Progressing Adleman's original
processing power. Computers are commonly knownresearch, their use of a biological computer allowed
to consist of integrated circuits mainly constructed offor the processing capacity to continue increasing
silicon; however, a computer is never considered tothrough the process of cell division.
be "alive." Technological advances however could useThe scientists in this experiment used three vertexes
the building blocks of our genome in creatingto perform their analysis. Using the bacteria
computer processors and data storage, and catapultEscherichia coli, commonly referred to as E-coli, the
processing speeds to incomprehensible levels notvertexes were assembled using a combination of
possible by today's standards.genes resulting in either a fluorescing green or red
DNA computing is an alternative to the waycolor. By randomly shuffling the DNA, the correct
computers work today. While this technology is notanswer, or route, would cause the bacteria to glow
readily available, or being mass produced, the theoryboth colors, giving it a yellow color. The results were
behind it is quite old and the development is ongoingverified by the scientists by ensuring the DNA
and catching more speed. Companies like IBM aresequence of the yellow bacteria was a result of
attempting to use DNA to produce the nextgenotypes representing a Hamiltonian path.
generation of processors.As can be seen with the bacterial computing
Before discussing how DNA can be used inexperiment and Adleman's experiment, there are
computers, it's important to first understand the basicseveral flaws with DNA computing. A major
structure of a DNA molecule. DNA is a doubledrawback is the need for human intervention.
stranded helix where the two strands are linked byProgramming the inputs for the DNA computer is a
base pairs of amino acids commonly labeled, A, T, C,complicated process. The scientists responsible for
and G. A single double helix strand has millions ofbuilding the bacteria computer were required to first
these connections which are limited as they onlyencode the DNA structure to reflect the 3 random
connect A to T and C to G. These amino acids wouldvertexes. Adleman had to first create DNA strings to
essentially take the place of the binary code of 1'srepresent the 7 vertexes for his experiment. The
and 0's used in computers today. The base pairs ofanalysis of the output as well requires human
amino acids are separated by.33 nanometers. To putinterpretation. Adleman was required to create a
the size into perspective, a DNA chip can be built in aseries of chemical reactions to abstract the
2-nanometer scale, when currently the top of the lineHamiltonian path strings, while the scientist in the
chip is built with a 45-nanometer node. To put thisbiological computer experiment needed to check for
another way, there are about 1 million gigabits ofyellow bacteria.
data per square inch of DNA. That figure explainsSo what exactly could a DNA computer do?
why the idea is being developed by companies likeObviously scientists are not simply trying to find the
IBM since this is 2000 times greater than our currentbest way to solve a Hamiltonian path problem, nor is
data storage systems. Jennifer Cha, as biochemist atit planned that the home computer is to be replaced
IBM indicated that "There is nothing else out thereby DNA powered processors. The concept of DNA
that we can do that with."computing is a highly debated topic. The research and
In 1994, Leonard Adleman, a professor at thedevelopment done thus far could open our world up
University of Southern California, first introduced thisto a new class of computing devices. One possibility
theory in an article in the journal Science. Adlemandiscussed is being able to apply tiny DNA computers
discussed using the DNA molecule in computing, andinside of the body to help monitor and prevent
demonstrated how it can be used to solve a sevendiseases. The computer would analyze conditions, and
point Hamiltonian path problem.make decisions based on their findings. Theoretically
In short, a Hamiltonian Path is a traceable path thatthe tiny DNA computer would be able to release
visits each vertex, or point, once with a beginningmedicine or kill diseased cells. The new processors
and ending point. While this may seem simple incould also take the place of the current day
theory, it is actually a complex problem to solve. Tosupercomputers used for data crunching in large
simplify this, if one was to try and plot the shortestcorporations, scientific labs, and government agencies.
route to tour the ten biggest cities in the UnitedProcessors faced with computing year's worth of
Kingdom only once, over 3.5 million routes would needdata could cut the processing time into a fraction of
to be analyzed. If this example were tested using awhat if currently takes.
single processor each of the 3.5 million scenariosDNA could also prove to be a much cheaper
would need to be calculated one at a time, and thealternative to our current data storage technology.
Hamiltonian Path would then be selected.One gram of genetic material, which is the size of
Rather than use ten vertexes Adleman used sevenone cubic centimeter, could hold the equivalent of 1
for his experiment. He encoded all the possibleTrillion compact discs. In a 2002 article of Business
solutions, both correct and incorrect, in a largeWeek the estimated cost of a DNA sequence
number of DNA. He labeled each of the seven citiesneeded for computing was $30, compared to the
in a four character combination of the base pairs of$500 Intel Pentium 4 chip.
amino acid found in DNA. An example of one cityThe use of DNA computing could finally dull Moore's
indicator would be TCGG. By mixing all of theLaw. Leonard Aldeman, the father of the ground
molecules in a test tube, he created all the DNAbreaking DNA computing work has said that "DNA
combinations, or answers, possible for the givenhas been storing the blueprint of life for several billion
conundrum. In theory this allowed for simultaneousyears. Its powers are an untapped legacy for the
processing in order to find the correct solution, as the21st century." The relatively young topic is a different
DNA strands were developing not in succession ofapproach to technology then we're currently used to
one another, but at the same time. Through a seriesseeing. The new area of research bridges the study
of chemical reactions, Adleman was able to removeof enzymology, nanotechnology, synthetic chemistry,
the incorrect answers and was able to leave onlyand computer science. Adleman believes, and hopes
those strands representing the correct Hamiltonianthat the research he began over 15 years ago can
path.unite the study of mathematics and biology and
Taking this one step further, a team of Unitedprovide the kind of focused progress witnessed
States scientists from universities across the nation,during the renaissance error by scientists like
recently were able to engineer bacteria in order toLeonardo DaVinci and Galileo.