PRINCETON, N.J. -- Princeton University researchers have developed a kind of
computer that uses the biological molecule RNA to solve complex problems. The
achievement marks a significant advance in molecular computing, an emerging
field in which scientists are harnessing molecules such as DNA and RNA to
solve certain problems more efficiently than could be done by conventional
computing.
In work to be published in the Proceedings of the National Academy of
Sciences, the Princeton scientists used a test tube containing 1,024
different strands of RNA to solve a simple version of the "knight problem," a
chess puzzle that is representative of a class of problems that requires
brute-force computing. The knight problem asks how many and where can one
place knights on a chessboard so they can not attack each other. For the
purposes of their experiment, the researchers restricted the board to just
nine squares, so there were 512 possible combinations. Of these, the RNA
computer correctly identified 43 solutions.
It also produced one incorrect response, highlighting the need to develop
error-checking techniques in chemical computing.
This test-tube computer does not have any immediate applications, and it will
probably never completely replace silicon technology. But it does have
attractive aspects, said assistant professor of ecology and evolutionary
biology Laura Landweber who led the research project in collaboration with
professor of computer science Richard Lipton, and postdoctoral fellow Dirk
Faulhammer and a student, Anthony Cukras.
"It begs the question, What is a computer?" said Landweber. "A computer can
be an abacus, it can be many types of devices. This is really an abstraction
of a computer."
One advantage, said Landweber, is that the genetic molecules DNA and RNA,
which encode all the instructions for creating and running life, can store
much more data in a given space than conventional memory chips. Another
benefit is that, with vast numbers of genetic fragments floating in a test
tube, a biomolecular computer could perform thousands or millions of
calculations at the same time. It is an extreme example of parallel
computing, which is a rapidly growing area of computer technology.
For example, in the knight problem, each strand of RNA represented a possible
solution, but the researchers did not need to sort through each one
individually; in a series of five steps, a specially targeted enzyme slashed
away all the strands that did not match the requirements of a correct
solution. Researchers believe that such techniques could be valuable for
problems that need to be solved by trial and error, where it is cumbersome to
test possible solutions one at a time.
DNA computing has attracted considerable attention from researchers since
1994 when Leonard Adleman of the University of Southern California used DNA
to solve a version of an archetypal problem called the traveling salesman
problem. The idea is that words written in the letters of DNA, referred to as
A, T, C and G, could represent the ones and zeroes used in computer logic.
Computing is accomplished by eliminating molecules whose sequences appear to
be poor solutions and retaining ones that seem more promising. The output of
final molecules can be read like the holes punched in an old-fashioned
computer tape.
Landweber found that substituting RNA for DNA gave her more flexibility in
developing a computing system. With DNA, there is a limited set of
restriction enzymes - a kind of molecular scissors - so scientists may not be
able to cut the molecule where they want. With RNA, Landweber's group could
use just one universal enzyme that targets any part of the molecule. This
aspect streamlines their approach and makes it inherently 'scalable' to
larger problems.
Editor's Note: The original news release can be found at
http://www.princeton.edu/pr/news/00/q1/0114-rna.htm
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