DNA computer

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As DNA , RNA or, more generally also Biocomputer be computer designated based on the use of the genetic material deoxyribonucleic acid (DNA) or ribonucleic acid based (RNA) as a storage and processing medium. They represent a field of bioelectronics .

The development of biocomputers is still in the early stages. The first theoretical impetus that data processing on the basis of biological molecules must be possible was provided by Nobel Prize winner Richard Feynman , founder of nanotechnology , in a lecture at the end of the 1950s.

history

The first thoughts on DNA storage had been going on since the 1960s and the first experiments since the turn of the millennium.

The original idea came from Leonard Adleman of the University of Southern California in 1994. Adleman proved in a proof of concept that you can use DNA for programming. This proof of concept consisted of using DNA to solve one stage of the Hamilton path problem. There has been great progress since Adleman’s first experiment and it was possible to prove that various Turing machines can be produced.

Initially, the interest in this then new technology was to solve " NP-difficult " problems. Very soon it was found out, however, that those problems might not be so easy to solve with the help of DNA computers and accordingly several "killer applications" have been proposed since then, which should prove its usefulness or its scope and thus its raison d'etre . In 1997, the computer scientist Mitsunori Ogihara, in collaboration with the biologist Animesh Ray, proposed such an application, which should be a proof of the applicability for Boolean functions , and described a possible implementation.

In 2002, scientists at the Weizmann Institute of Science in Rehovot, Israel, built a programmable molecular computer made of enzymes and DNA molecules instead of silicon chips. On April 28, 2004, Ehud Shapiro , Yaakov Benenson, Binyamin Gil, Uri Ben-Dor and Rivka Adar from the Weizmann Institute announced in the journal Nature that they had built a DNA computer coupled with an input and output module, which should be able to detect cancer activity in a cell and deliver a drug when it occurs.

In 2011, the bioinformatician Nick Goldman came up with the idea of ​​storing amounts of data in DNA. Two years later (January 2013) researchers managed to save all Shakespeare sonnets and the speech I Have a Dream by Martin Luther King on the DNA. Meanwhile, other media files like PDF, photos, audio files and bitcoins have also been saved.

In 2012 Robert Grass and his colleagues managed to save and access a copy of the Swiss Federal Letter.

In March 2013, scientists built a biological transistor called a “transcriptor”.

The University of Washington is researching together with Microsoft to use DNA as a storage medium. In this way, data should remain legible for centuries and the area of ​​a data center should be reduced to a cube. Data is automatically filed in artificially produced DNA strands and later retrieved. The four bases adenine (A), cytosine (C), guanine (G) and thymine (T) are encoded in a binary code by software. A synthesis machine takes over the chemical production of the DNA strands . When the data is retrieved, the base sequences of the DNA strands and are translated into binary code. However, the reading speed has been very slow so far and the coding of the word Hello already takes 21 hours.

At the beginning of July 2019, a DNA startup managed to save the entire English-language Wikipedia with a size of approx. 16 gigabytes on DNA strands.

idea

The organization and complexity of all living things are based on coding with four different bases in the DNA molecule. As a result, the DNA represents a medium that is perfectly suited for data processing. According to various calculations, a DNA computer with a volume of liquid of one liter and six grams of DNA contained in it would give a theoretical storage capacity of 3072 exabytes . The theoretically achievable speed due to the massive parallelism of the calculations would also be enormous. There are about a thousand peta operations per second, while the most powerful computers today achieve a few ten peta operations per second.

techniques

There are several methods of building a DNA computer-like device. Each of these methods had their own advantages and disadvantages. Most build the basic logic gates (AND, OR, NOT), which are known from the digital world and Boolean algebra, on a DNA basis. Some of these bases include DNAzymes, deoxyoligonucleotides, enzymes and polymerase chain reactions.

Toehold Exchange

DNA computers were built using the “toehold exchange concept”, among other things. During this process, a strand of DNA is attached to a sticky end , also known as a toehold, on another DNA molecule. This can then cause another strand to be misplaced as well. This allows you to develop modular logic components such as AND, OR, non-gates and signal amplifiers that can be connected to computers of any size. This DNA computer doesn't need enzymes or any of the chemical properties of DNA.

Examples

In 1994 Leonard Adleman presented his TT-100, the first prototype of a DNA computer in the form of a test tube with 100 microliters of DNA solution. With the help of this device, he was able to solve simple math problems through the free reaction of DNA.

In another experiment, a simple variant of the traveling salesman problem was solved using a DNA computer. For this purpose, a type of DNA fragment was generated for each city to be visited. Such a DNA fragment is capable of binding to other such DNA fragments. These DNA fragments were actually made and mixed together in a test tube . Within seconds, larger DNA fragments were created from the smaller DNA fragments, which represented different travel routes. A chemical reaction (which lasted days) eliminated the DNA fragments that represented longer travel routes. The solution to this problem remained, but it cannot be evaluated with today's means. So this experiment is not really applicable, but a proof of concept .

In another experiment, researchers want to make DNA conductive with traces of gold so that it can be used as a circuit. When used as a storage medium, the sequence of 0 and 1 should be represented by two of the four bases guanine , adenine , cytosine and thymine .

Due to their special resistance to the damaging effects of all kinds of Deinococcus radiodurans bacteria, they could be used as DNA storage. American computer scientists translated the text of the English nursery rhyme It's a Small World into the genetic code and smuggled the corresponding DNA sequence into the genetic material of the bacteria. Even after about a hundred generations of bacteria, the stanzas could be read out again in unchanged form using standard sequencing technology , i.e. That is, the information introduced was stored in a stable manner and, in addition, the multiplication of the bacteria increased their redundancy.

application

It is predicted that DNA computers will be able to deliver new solutions especially where they differ from traditional computers: in terms of storage capacity and parallelization .

The realization of the DNA computer is currently failing mainly due to technical problems. The aim of current research is to create a hybrid system in which electronic assemblies are connected upstream of the DNA technology.

Alternative technologies

In 2009, IBM entered into a partnership with CalTech , whose goal is to create DNA chips. A CalTech working group is already working on the fabrication of the circuits that are operated with nucleic acids. One of these chips can calculate whole square roots. Furthermore, a compiler has already been written in Perl .

Advantages and disadvantages

The fact that the DNA computer only produces responses very slowly (the reaction time of the DNA is measured in seconds, hours or even days, instead of the usual milliseconds) and therefore has a long read and write speed, is compensated for by the fact that Many invoices run in parallel and thus the complexity of the task at hand has little effect on the calculation time. This can be explained by the fact that several million or billions of molecules interact with one another at the same time. However, it has been far more difficult to evaluate the results of a DNA computer than of a digital one.

Furthermore, DNA computers are not very practical because the storage units are often very small and can only be processed in a complicated manner. Data can also be damaged by UV radiation more quickly than with conventional storage media. On the other hand, the advantages mentioned are a generally longer service life, higher storage capacity with less storage space ("the entire Internet fits the size of a shoebox"), lower power consumption and increased data security and protection against hacker attacks. The high costs are also a problem, for example DNA synthesis costs around 7,000 US dollars for two megabytes and reading another 2,000 or 40 cents per byte. Up to 215 petabytes should fit on one gram of genetic material.

See also

literature

  • Thomas Buchholz, Martin Kutrib: Molecular Computer. Calculating in the test tube . In: Spiegel der Forschung 15 (1998), Issue 1, pp. 27–36 ( full text )
  • Robert Ludlum : The Paris Option . ISBN 3-453-43015-8 (belletristic representation)
  • Ralf Zimmer: A universal DNA computer . In: Der GMD-Spiegel ISSN  0724-4339 , Issue 3/4, October 1999, pp. 24-28
  • Leonard M. Adleman : Calculating with DNA . In: Spectrum of Science Dossier - Computer Architectures, 4/2000, pp. 50–57. (Adleman is the A in RSA ).
  • Zoya Ignatova, Israel Martinez-Perez, Karl-Heinz Zimmermann : DNA Computing Models. ISBN 978-0-387-73635-8 , Springer, XIV, 288 p., 20 Illus., 2008.

Web links

Individual evidence

  1. a b c d Radiation-resistant bacteria as permanent data storage - netzeitun… February 11, 2013, archived from the original on February 11, 2013 ; accessed on June 12, 2019 .
  2. ^ Leonard M. Adleman (1994): Molecular Computation of Solutions to Combinatorial Problems. Science 266: 1021-1024. doi : 10.1126 / science.7973651
  3. ^ Dan Boneh, Christopher Dunworth, Richard J. Lipton, Jir̆í Sgal (1996): On the computational power of DNA. Discrete Applied Mathematics Volume 71, Issues 1-3: 79-94. doi : 10.1016 / S0166-218X (96) 00058-3
  4. Lila Kari, Greg Gloor, Sheng Yu: Using DNA to solve the Bounded Post Correspondence Problem . In: Theoretical Computer Science . 231, No. 2, January 2000, pp. 192-203. doi : 10.1016 / s0304-3975 (99) 00100-0 . - Describes a solution for the bounded post correspondence problem , a hard-on-average NP-complete problem. Also available here: http://www.csd.uwo.ca/~lila/pdfs/Using%20DNA%20to%20solve%20the%20Bounded%20Post%20Correspondence%20Problem.pdf
  5. M. Ogihara and A. Ray (1999): Simulating Boolean circuits on a DNA computer. Algorithmica 25: 239-250. Download PDF
  6. "In Just a Few Drops, A Breakthrough in Computing" , New York Times , May 21, 1997
  7. Stefan Lövgren: Computer Made from DNA and Enzymes . In: National Geographic . February 24, 2003. Retrieved November 26, 2009.
  8. Yaakov Benenson, Binyamin Gil, Uri Ben-Dor, Rivka Adar, Ehud Shapiro (2004): An autonomous molecular computer for logical control of gene expression. Nature 429: 423-429 doi : 10.1038 / nature02551
  9. Jochen Siegle: DNA: Microsoft automates data storage in biomolecules . March 29, 2019, ISSN  0376-6829 ( nzz.ch [accessed June 12, 2019]).
  10. ^ Microsoft and University of Washington researchers set record for DNA storage. July 7, 2016, Retrieved June 12, 2019 (American English).
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  12. futurezone / PR: Storage of the future: Microsoft's artificial DNA says "Hello". Retrieved June 12, 2019 .
  13. René Resch: Complete Wikipedia stored on DNA strands. July 1, 2019, accessed on July 3, 2019 (German).
  14. Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree (2006): Enzyme-Free Nucleic Acid Logic Circuits. Science 314: 1585-1588. doi : 10.1126 / science.1132493
  15. Archive link ( Memento from October 14, 2011 in the Internet Archive ) (journal du CalTech)
  16. http://www.sciencemag.org/content/332/6034/1196.abstract
  17. http://www.dna.caltech.edu/SeesawCompiler
  18. Bioinformaticians: "You can't hack DNA memories" - derStandard.de. Retrieved July 17, 2019 (Austrian German).
  19. Storage technology: Microsoft introduces automatic DNA storage - Golem.de. Accessed June 12, 2019 (German).
  20. DNA as data storage. July 13, 2017. Retrieved July 17, 2019 .
  21. ZDB catalog - search results page: iss = "0174-4909". Retrieved July 17, 2019 .
  22. Annett Stein: DNA: Researchers create memories with extremely high data density . March 6, 2017 ( welt.de [accessed June 12, 2019]).
  23. Jan Oliver Löfken: Data storage: hard drives made of DNA store more than any chip . In: The time . March 3, 2017, ISSN  0044-2070 ( zeit.de [accessed June 12, 2019]).
  24. Storage technology: Microsoft stores data in artificial DNA. Retrieved June 12, 2019 .