It is believed that DNA will save us from computers. Thanks to advances in the replacement of silicon transistors, computers based on DNA promise to provide us a massive parallel computing architecture, is impossible at the present time. But here’s the catch: the molecular circuits that were created before today, had absolutely no flexibility. Today, the use of DNA for computing is the same as the “create new computer from new hardware to run only one program,” says David Doty.
Doty, Professor, University of California at Davis, and his colleagues decided to find out what it would take to create a DNA computer that actually can be reprogrammed.
The computer of DNA
In an article published this week in the journal Nature, Doty and his colleagues at the University of California and the University of Maynooth has demonstrated just that. They showed that it is possible to use a simple trigger to make the same basic set of DNA molecules to implement many different algorithms. Although this study is still exploratory in nature, in the future can be used reprogrammable algorithms for molecular programming DNA robots that have successfully delivered drugs to the cancer cells.
“This is one of the most important works in the field,” says Thorsten-Lars Schmidt, associate Professor of experimental Biophysics at Kent state University who did not participate in the study. “Earlier it was algorithmic self-Assembly, but not to this degree of complexity”.
In electronic computers it seems that you are using to read this article, bits — binary units of information that tell the computer what to do. They represent discrete physical state of the underlying hardware, usually in the form of the presence or absence of electric current. These bits — or even an electric signal which is transmitted through the circuit consisting of logic elements that perform an operation on one or more input bits and produce one bit as output.
Combining these simple building blocks again and again, computers can run a surprisingly complex program. The idea behind DNA-based computing, is to replace the chemical bonds electrical signals and nucleic acid — silicon, and to create biomolecular software. According to Eric Winfrey, a computer scientist from Caltech and co-author of the work, molecular algorithms use the natural ability of information processing, sewn into the DNA, but instead to give control to nature, “the growth process is controlled by computers”.
Over the last 20 years in several experiments, we used molecular algorithms for things such as TIC-TAC-toe or Assembly of various shapes. In each of these cases, the DNA sequence had to be carefully designed to create one specific algorithm that would generate the structure of DNA. What’s different in this case is the fact that researchers have developed a system in which the same underlying DNA fragments can be sequenced to create an entirely different algorithms and therefore can be made of different end products.
This process begins with DNA origami, a method of folding a long piece of DNA into a desired shape. This rolled-up piece of DNA serves as a “led” (seed, seed), which runs an algorithmic pipeline, like on a string dipped in sugared water, gradually grows the caramel. The seed remains largely the same irrespective of the algorithm and changes are made only in a few small sequences for each new experiment.
After scientists created the seed, they added in a solution of 100 other strands of DNA, DNA fragments. These fragments, each of which consists of a unique arrangement 42 of the nucleic bases (the four basic biological molecules that comprise DNA) taken from a large collection of 355 fragments of DNA created by scientists. To create another algorithm scientists have to choose a different set of starting fragments. Molecular algorithm that includes random walk requires a different set of DNA fragments that the algorithm uses for calculation. Since these DNA fragments are joined in the Assembly process, they form a circuit that implements the selected molecular algorithm on the input bits provided by the led.
Using this system, scientists have created 21 different algorithm, which can perform tasks such as recognizing a multiple of three, the choice of leader, generation patterns, and the score to 63. All these algorithms were implemented using different combinations of the same 355 DNA fragments.
Of course, to write code by resetting of DNA fragments in a test tube while it does not, however, the whole idea is a model for future iterations of flexible computers based on DNA. If Doty, Winfrey and woods get their way, molecular programmers of tomorrow even won’t think about the biomechanics underlying their programs, just as modern programmers do not have to understand the physics of transistors to write good software.
The potential use of this nano-scale Assembly technique of the imagination, but these projections are based on our relatively limited understanding of the nanoscale world. Alan Turing was not able to predict the advent of the Internet, and therefore we may have incomprehensible the application of molecular Informatics.
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