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[tehra]

Thursday November 22, 12:28 AM

Scientists build tiny computer from DNA
By Patricia Reaney


LONDON (Reuters) - Following Mother Nature's lead, Israeli scientists have built a DNA computer so tiny that a trillion of them could fit in a test tube and perform a billion operations per second with 99.8 percent accuracy.


Instead of using figures and formulas to solve a problem, the microscopic computer's input, output and software are made up of DNA molecules -- which store and process encoded information in living organisms.


Scientists see such DNA computers as future competitors to for their more conventional cousins because miniaturisation is reaching its limits and DNA has the potential to be much faster than conventional computers.


"We have built a nanoscale computer made of biomolecules that is so small you cannot run them one at a time. When a trillion computers run together they are capable of performing a billion operations," Professor Ehud Shapiro of the Weizmann Institute in Israel told Reuters on Wednesday.


It is the first programmable autonomous computing machine in which the input, output, software and hardware are all made of biomolecules.


Although too simple to have any immediate applications it could form the basis of a DNA computer in the future that could potentially operate within human cells and act as a monitoring device to detect potentially disease-causing changes and synthesise drugs to fix them.


The model could also form the basis of computers that could be used to screen DNA libraries in parallel without sequencing each molecule, which could speed up the acquisition of knowledge about DNA.


ENORMOUS POTENTIAL


DNA can hold more information in a cubic centimetre than a trillion CDs. The double helix molecule that contains human genes stores data on four chemical bases -- known by the letters A, T, C and G -- giving it massive memory capability that scientists are only just beginning to tap into.


"The living cell contains incredible molecular machines that manipulate information-encoding molecules such as DNA and RNA (its chemical cousin) in ways that are fundamentally very similar to computation," said Shapiro, the head of the research team that developed the DNA computer.


"Since we don't know how to effectively modify these machines or create new ones just yet, the trick is to find naturally existing machines that, when combined, can be steered to actually compute," he added.


Writing in the science journal Nature, Shapiro and his team describe their DNA computer, which is a molecular model of one of the simplest computing machines -- the automaton which can answer certain yes or no questions.


Data is represented by pairs of molecules on a strand of DNA and two naturally occurring enzymes act as the hardware to read, copy and manipulate the code.


When it is all mixed together in the test tube, the software and hardware operate on the input molecule to create the output.


The DNA computer also has a very low energy consumption, so if it is put inside the cell it would not require much energy to work.


DNA computing is a very young branch of science that started less than a decade ago, when Leonard Adleman of the University of Southern California pioneered the field by using DNA in a test tube to solve a mathematical problem.


Scientists around the globe are now trying to marry computer technology and biology by using nature's own design to process information.

[Cyto]

DNA forms building block for next breed of computer

By Jonathan Sidener
UNION-TRIBUNE STAFF WRITER

September 1, 2003

A snip...

"You can't compare and say a DNA computer is or isn't faster than this," Keinan said, gesturing toward a sleek, metallic Macintosh PowerBook in his Scripps office. "It's a different type of computer."

DNA computers don't have keyboards and monitors. The computing takes place on the laboratory bench as complex molecular-chemical reactions.

The first calculations, nearly 10 years ago, took place inside beakers and test tubes.

A new generation of DNA computing uses biochips, devices built using semiconductor manufacturing technology. A biochip has millions of pieces of DNA on its surface instead of the millions of electronic circuits on a computer chip.

At the moment, DNA computers are laboratory curiosities. One computer can play a respectable game of tick-tack-toe. Another can solve chess riddles. The computations they handle would make the least powerful of today's computers yawn.

But DNA computers show some intriguing qualities.

DNA is extremely efficient, both in storing data and in its use of energy. One gram of DNA, which would take up about as much space as an ice cube, can hold as much information as 1 trillion compact discs.

With today's computer chips, energy consumption and the heat produced as a byproduct can cause malfunctions. But the chemical reactions that make a DNA computer work require little energy.

Most significantly, the biomolecular computers operate on different underlying principles.

Electronic computers make their calculations by processing a series of zeroes and ones, or binary code, one character at a time in a rapid sequence, like a machine gun that fires a series of bullets from a single barrel in succession.

Not so with DNA computers. Because millions of DNA snippets can fit into a drop of water, DNA computers can make many parallel calculations at once, more comparable to a shrapnel grenade that launches many projectiles at the same instant.

To Keinan and other researchers, this parallel processing provides much of the allure of DNA computing, the idea that machines built with a fundamentally different computing engine will be able to tackle fundamentally different questions.

[Cyto]

Purdue Researchers Stretch DNA On Chip, Lay Track For Future Computers
10/08/2003 -- Researchers at Purdue University are making it easier to read life's genetic blueprint.

They have precisely placed strands of DNA on a silicon chip and then stretched out the strands so that their encoded information might be read more clearly, two steps critical to possibly using DNA for future electronic devices and computers.

Findings about the research are detailed in a paper posted online this month and will appear in an upcoming issue of the journal Advanced Materials. The paper was written by Albena Ivanisevic, an assistant professor of biomedical engineering at Purdue, and physics graduate student Dorjderem Nyamjav.

Ivanisevic and Nyamjav created templates containing charged lines of commercially available polymer. The positively charged polymer has the opposite charge as DNA, so when the genetic material is dropped onto the chip, it is attracted to the lines automatically. Then the researchers used a syringe to drag the DNA, uncoiling the strands along the template surface.

"The charged structures enable us to direct biological molecules in a certain location," Ivanisevic said.

Although other researchers have deposited DNA onto similar templates, Ivanisevic is the first to demonstrate how to also stretch strands of DNA in specific locations on such templates, which contain features so small they are measured in nanometers. This step could lead to the ability to stretch DNA molecules in specific locations on electronic chips, which is critical in harnessing the storage capacity of DNA for future computers.

"We don't want to have DNA coiled on the surface," Ivanisevic said. "We want to be able to extend it and stretch it so that you can read what's on the strand. You can think about a variety of DNA computing strategies. But you have to have the strand extended, and you have to have the ability to place it in a specific location."

Researchers also would like to be able to place DNA strands directly between two electrodes to perform consistent, precise measurements and determine certain electronic characteristics of genetic material.

"If you can actually demonstrate that you can do that, then you can think about making real molecular devices where DNA is used as a construction material," Ivanisevic said. "At this point, however, this is certainly a very basic nanofabrication problem."

Theoretically, future computers might tap the vast storage capacity that enables DNA to hold the complex blueprints of living organisms. These new computers would be based on DNA's four-letter code instead of a computer's customary two digits and would offer advantages in speed, memory capacity and energy efficiency over conventional electronics for solving certain types of complex problems. (In theory)

The researchers used an instrument called an atomic force microscope and a device called a cantilever to lay down the lines of polymer in a process called dip-pen nanolithography. Each of the lines of polymer is about as wide as 100 nanometers, and each centimeter-square chip contains numerous templates.

"Nano" is a prefix meaning one-billionth, so a nanometer is one-billionth of a meter, or roughly the length of 10 hydrogen atoms strung together. A single DNA molecule is about 2 nanometers wide.

The same technique can be used to precisely place a variety of biological molecules, including proteins and viruses, onto such templates. It is not necessary to dry out or stain the molecules, meaning they can be kept in their natural state and still function as they would in living organisms.

Because the polymer is commercially available, the procedure can be readily studied by researchers and industry.

Ivanisevic is associated with two centers in Purdue's Discovery Park: the Birck Nanotechnology Center and Bindley Bioscience Center, which funded the research.

Writer: Emil Venere, (765) 494-4709, venere@purdue.edu
Source: Albena Ivanisevic, (765) 496-3676, albena@purdue.edu
Purdue News Service: (765) 494-2096; purduenews@purdue.edu
Source: Purdue University