Source : Scripps Research Institute
LA
JOLLA, CA – February 7, 2010 – Scientists at The Scripps Research Institute in
California and the Technion–Israel Institute of Technology have developed a
“biological computer” made entirely from biomolecules that is capable of
deciphering images encrypted on DNA chips. Although DNA has been used for
encryption in the past, this is the first experimental demonstration of a
molecular cryptosystem of images based on DNA computing.
The
study was published in a recent online-before-print edition of the journal Angewandte
Chemie.
Instead
of using traditional computer hardware, a group led by Professor Ehud Keinan of
Scripps Research and the Technion created a computing system using
bio-molecules. When suitable software was applied to the biological computer,
it could decrypt, separately, fluorescent images of The Scripps Research
Institute and Technion logos.
A
Union Between Biology and Computer Science
In
explaining the work’s union of the often-disparate fields of biology and
computer science, Keinan notes that a computer is, by definition, a machine made
of four components—hardware, software, input, and output. Traditional computers
have always been electronic, machines in which both input and output are
electronic signals. The hardware is a complex composition of metallic and
plastic components, wires, and transistors, and the software is a sequence of
instructions given to the machine in the form of electronic signals.
“In
contrast to electronic computers, there are computing machines in which all
four components are nothing but molecules,” Keinan said. “For example, all
biological systems and even entire living organisms are such computers. Every
one of us is a biomolecular computer, a machine in which all four components
are molecules that ‘talk’ to one another logically.”
The
hardware and software in these devices, Keinan notes, are complex biological
molecules that activate one another to carry out some predetermined chemical
work. The input is a molecule that undergoes specific, predetermined changes,
following a specific set of rules (software), and the output of this chemical
computation process is another well-defined molecule.
“Building”
a Biological Computer
When
asked what a biological computer looks like, Keinan laughs.
“Well,”
he said, “it’s not exactly photogenic.” This computer is “built” by combining
chemical components into a solution in a tube. Various small DNA molecules are
mixed in solution with selected DNA enzymes and ATP. The latter is used as the
energy source of the device.
“It’s
a clear solution—you don’t really see anything,” Keinan said. “The molecules
start interacting upon one another, and we step back and watch what happens.”
And by tinkering with the type of DNA and enzymes in the mix, scientists can
fine-tune the process to a desired result.
“Our
biological computing device is based on the 75-year-old design by the English mathematician, cryptanalyst, and computer scientist Alan Turing,”
Keinan said. “He was highly influential in the development of computer science, providing a
formalization of the concepts of algorithm and computation,
and he played a significant role in the creation of the modern computer. Turing
showed convincingly that using this model you can do all the calculations in
the world. The input of the Turing machine is a long tape containing a series
of symbols and letters, which is reminiscent of a DNA string. A reading head
runs from one letter to another, and on each station it does four actions: 1)
reading the letter; 2) replacing that letter with another letter; 3) changing
its internal state; and 4) moving to next position. A table of instructions,
known as the transitional rules, or software, dictates these actions. Our
device is based on the model of a finite state automaton, which is a simplified
version of the Turing machine. “
Unique
Biological Properties
Now
that he has shown the viability of a biological computer, does Keinan hope that
this model will compete with its electronic counterpart?
“The
ever-increasing interest in biomolecular computing devices has not arisen from
the hope that such machines could ever compete with electronic computers, which
offer greater speed, fidelity, and power in traditional computing tasks,”
Keinan said. “The main advantages of biomolecular computing devices over
electronic computers have to do with other properties.”
As
shown in this work, he continues, a wealth of information can be stored and
encrypted in DNA molecules. Although each computing step is slower than the
flow of electrons in an electronic computer, the fact that trillions of such
chemical steps are done in parallel makes the entire computing process fast.
“Considering the fact that current microarray technology allows for printing
millions of pixels on a single chip, the numbers of possible images that can be
encrypted on such chips is astronomically large,” he said.
“Also,
as shown in our previous work and other projects carried out in our lab, these
devices can interact directly with biological systems and even with living
organisms,” Keinan explained. “No interface is required since all components of
molecular computers, including hardware, software, input, and output, are
molecules that interact in solution along a cascade of programmable chemical
events.” He adds that because of DNA’s ability to store information, major
computer companies have been extremely interested in the development of
DNA-based computing systems.
The
first author of the study, “A Molecular Cryptosystem for Images by DNA
Computing,” is graduate student Sivan Shoshani of Technion. In addition to
Keinan and Shoshani, authors include postdoctoral fellow Ron Piran of Scripps
Research and Yoav Arava of the Technion. For more information on the paper, see
Angewandte Chemie at http://onlinelibrary.wiley.com/doi/10.1002/anie.201107156/abstract
This
work was supported by the National Science Foundation, the Israel-US Binational
Science Foundation, and the Skaggs Institute for Chemical Biology, as well as
graduate fellowships from the Irwin and Joan Jacobs Foundation, the Fine Foundation,
the Russell Berrie Nanotechnology Institute, and the Israel Ministry of Science
and Technology.
About The Scripps Research Institute
The Scripps Research Institute is one of the world's largest independent, non-profit biomedical research organizations. Scripps Research is internationally recognized for its discoveries in immunology, molecular and cellular biology, chemistry, neuroscience, and vaccine development, as well as for its insights into autoimmune, cardiovascular, and infectious disease. Headquartered in La Jolla, California, the institute also includes a campus in Jupiter, Florida, where scientists focus on drug discovery and technology development in addition to basic biomedical science. Scripps Research currently employs about 3,000 scientists, staff, postdoctoral fellows, and graduate students on its two campuses. The institute's graduate program, which awards Ph.D. degrees in biology and chemistry, is ranked among the top ten such programs in the nation. For more information, see www.scripps.edu.
# # #