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DNA as computer

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Researchers have shown off a "DNA computer" of unprecedented complexity, which can calculate square roots.


DNA computing uses chemical reactions to solve problems in which a number of DNA strands act as "bits".


The work, reported in Science, required 130 strands of DNA to work in a cascade of programmed chemical changes.


The approach is not designed to rival traditional electronics, but rather to allow computing to occur in biological contexts, perhaps even in the body.


DNA computing was first proposed by Leonard Adelman in 1994, to solve what is known as the "travelling salesman problem" - determining the shortest path that joins a number of geographically separated locations.


Since then, a wide array of approaches has aimed to make use of the properties that make DNA attractive for computing: it can be made to order and its interactions with itself are well-studied and reliable.


In 2006, Erik Winfree of the California Institute of Technology (Caltech) and his colleagues published an article in Science a framework making use of one of these approaches, known as strand displacement.


Stretches of DNA made of just one strand (rather than the two joined strands that form the well-known double helix) were used as anchor points for other single strands.


Now, Professor Winfree and his collaborator Lulu Qian have employed a scheme using what they call "seesaw gates", which accomplish the shuffling and exchange of DNA strands using simpler machinery.


The work showed that seesaw gates could again be used to create logic gates - the basis of electronic computing's manipulation of information - and represented a five-fold leap in the number of DNA sections ever implemented in such a DNA computer.


The approach can be scaled up in complexity far further, the authors suggest - but the process is slow.


For example, it was used to calculate the square root of a four-bit number, but the process took between six and 10 hours.


However, Professor Winfree said that contrary to conventional electronics, the goal is not just high speeds.


"We are no longer pursuing the goal targeted by Len Adleman's original DNA computing experiment: to compete with silicon by using the massive parallelism of chemistry to solve combinatorial problems in mathematics," he explained.


"Instead, our goal is now - and has been for many years - to enrich chemistry itself so that molecular behaviours can be programmed.


"We'd like to make chemical systems that can probe their molecular environments, process chemical signals, make decisions, and take actions at the chemical level."





Abstract of paper:



Science 3 June 2011:

Vol. 332 no. 6034 pp. 1196-1201

DOI: 10.1126/science.1200520


Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

Lulu Qian1 and Erik Winfree1,2,3,*

+ Author Affiliations


1Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA.

2Computer Science, California Institute of Technology, Pasadena, CA 91125, USA.

3Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA.




To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.






impressive work. the doors were made by someone else, but this really gets them open.

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I've been hearing talk of biological computing for a while. From what I know scientists are trying to work on using e. coli in processing. Should be neat.

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Researchers have figured out that data can be stored in bacteria, and that a single gram of bacteria can store more information than a giant 900 terabyte hard drive! This storing and encrypting information in living organisms is called biostorage, and students at Hong Kong's Chinese University are using E. coli to test the possibilities of how we store information in the future.


You could one day keep a box of E. coli bacteria in your fridge, but rather than storing just the potential for food poisoning, you'll be storing piles of information.


Discovery News reports that the concept started several years ago.


"In 2007, a team at Japan's Keio University said they had successfully encoded the equation that represents Einstein's theory of relativity, E=MC², in the DNA of a common soil bacterium. They pointed out that because bacteria constantly reproduce, a group of the single-celled organisms could store a piece of information for thousands of years."






"It is a commonplace metaphor that the genome is the operating system of a living organism. We wanted to see if the analogy actually holds up."







and this is a nice comprehensive e coli article:




It is widely known for causing outbreaks of infectious diarrhoea and is currently held responsible for a number of deaths - but some scientists say E. coli has given us the answer to life itself.

'Micro Factories'

'Birth of biotechnology'

'Green fuel'

'Living Computers'

'Sinister side'

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