Play Video
1
Michio Kaku: Tweaking Moore
Michio Kaku: Tweaking Moore's Law and the Computers of the Post-Silicon Era
::2012/04/13::
Play Video
2
Using Your DNA as a Hard Drive
Using Your DNA as a Hard Drive
::2013/01/25::
Play Video
3
DNA AS COMPUTER-LIKE REWRITABLE DATA STORAGE
DNA AS COMPUTER-LIKE REWRITABLE DATA STORAGE
::2012/05/22::
Play Video
4
Mod-09 Lec-41 DNA COMPUTING
Mod-09 Lec-41 DNA COMPUTING
::2011/10/05::
Play Video
5
What is DNA computing?
What is DNA computing?
::2013/04/27::
Play Video
6
DNA Transistor
DNA Transistor
::2009/10/05::
Play Video
7
DNA Computing
DNA Computing
::2012/07/24::
Play Video
8
DNA and Computers
DNA and Computers
::2007/08/16::
Play Video
9
Quantum and DNA computers : future of computing?
Quantum and DNA computers : future of computing?
::2010/12/17::
Play Video
10
Aaron Wilson
Aaron Wilson's Intro to DNA Computing
::2012/04/12::
Play Video
11
Don
Don't Panic - Episode #9 - On DNA Computing, Hyperloop Hype and iPhone Puzzles
::2013/08/19::
Play Video
12
Preventing rape in the military through effective DNA computing
Preventing rape in the military through effective DNA computing
::2014/05/09::
Play Video
13
DNA Computing Systems : All About Data Encryption
DNA Computing Systems : All About Data Encryption
::2011/04/29::
Play Video
14
Programming Nanoscale Structure Using DNA-Based Information
Programming Nanoscale Structure Using DNA-Based Information
::2013/06/14::
Play Video
15
DNA Computing Intro!
DNA Computing Intro!
::2013/05/07::
Play Video
16
Small Business Cloud Computing by DNA Computing Systems
Small Business Cloud Computing by DNA Computing Systems
::2011/10/21::
Play Video
17
Benefits of Using an MSP - DNA Computing Systems  Houston
Benefits of Using an MSP - DNA Computing Systems Houston
::2011/03/01::
Play Video
18
The Biggest Mistake in Business IT, Presented by DNA Computing Systems
The Biggest Mistake in Business IT, Presented by DNA Computing Systems
::2011/08/23::
Play Video
19
COMPUTER ENGINEERING VIDEO TUTORIAL 41 DNA COMPUTING
COMPUTER ENGINEERING VIDEO TUTORIAL 41 DNA COMPUTING
::2014/09/22::
Play Video
20
Strange Computer Code Discovered Concealed In Superstring Equations!
Strange Computer Code Discovered Concealed In Superstring Equations!
::2012/03/21::
Play Video
21
floorspeed dna computers
floorspeed dna computers
::2011/08/07::
Play Video
22
DNA: Without Excuse
DNA: Without Excuse
::2010/05/03::
Play Video
23
Classical and Quantum Information in DNA (Google Workshop on Quantum Biology)
Classical and Quantum Information in DNA (Google Workshop on Quantum Biology)
::2010/10/28::
Play Video
24
Company Profile DNA Computer
Company Profile DNA Computer
::2012/10/19::
Play Video
25
NANOTECHNOLOGY -  Nanomedicine DNA and Gold Nanoparticles (Lecture - 7)
NANOTECHNOLOGY - Nanomedicine DNA and Gold Nanoparticles (Lecture - 7)
::2013/07/09::
Play Video
26
DNA gel electrophoresis lab demo
DNA gel electrophoresis lab demo
::2012/09/14::
Play Video
27
Jonathan Weissman (UCSF/HHMI): DNA Sequencing
Jonathan Weissman (UCSF/HHMI): DNA Sequencing
::2011/01/09::
Play Video
28
TrueAllele® Computing: All the DNA, all the time
TrueAllele® Computing: All the DNA, all the time
::2014/07/31::
Play Video
29
Cells Injected With DNA By Computer To Create Self-Replicating Lifeforms
Cells Injected With DNA By Computer To Create Self-Replicating Lifeforms
::2010/05/20::
Play Video
30
Personal Genome Computing: Breakthroughs, Risks and Opportunities
Personal Genome Computing: Breakthroughs, Risks and Opportunities
::2009/02/02::
Play Video
31
How Point of Care Diagnostics Will Change Health Care, Texas Enteprise Speaker Prof.Andrew Ellington
How Point of Care Diagnostics Will Change Health Care, Texas Enteprise Speaker Prof.Andrew Ellington
::2012/05/15::
Play Video
32
DNA Consumer Products: Not as Far Out as You Think
DNA Consumer Products: Not as Far Out as You Think
::2013/06/05::
Play Video
33
Paul Rothemund: The astonishing promise of DNA folding
Paul Rothemund: The astonishing promise of DNA folding
::2008/09/04::
Play Video
34
James Watson: How we discovered DNA
James Watson: How we discovered DNA
::2007/05/16::
Play Video
35
Living Computer Created With Slime Mold?
Living Computer Created With Slime Mold?
::2013/06/25::
Play Video
36
Modern Day Mapmakers: DNA Sequencing and Other Technologies
Modern Day Mapmakers: DNA Sequencing and Other Technologies
::2014/09/26::
Play Video
37
Craig Venter: A voyage of DNA, genes and the sea
Craig Venter: A voyage of DNA, genes and the sea
::2007/05/02::
Play Video
38
Drug delivery and DNA nanotechnology
Drug delivery and DNA nanotechnology
::2013/11/06::
Play Video
39
July 19, 2013: Age Effects on DNA Methylation Models
July 19, 2013: Age Effects on DNA Methylation Models
::2013/10/16::
Play Video
40
Great Principles of Computing - Peter J. Denning
Great Principles of Computing - Peter J. Denning
::2007/11/15::
Play Video
41
The DNA of Neanderthal people - Part 2
The DNA of Neanderthal people - Part 2
::2014/06/17::
Play Video
42
Andrew Hessel on DNA
Andrew Hessel on DNA
::2009/11/07::
Play Video
43
Michael Schatz: DNA In the Cloud
Michael Schatz: DNA In the Cloud
::2012/03/10::
Play Video
44
4 Tips for Picking a Secure Password
4 Tips for Picking a Secure Password
::2011/03/31::
Play Video
45
Cloud Computing in 90 Seconds!
Cloud Computing in 90 Seconds!
::2011/09/06::
Play Video
46
Bio-molecular Computing
Bio-molecular Computing
::2012/06/17::
Play Video
47
Houston Tech Support - 5 Important Tips
Houston Tech Support - 5 Important Tips
::2011/06/22::
Play Video
48
Rasmus Nielsen - Berkeley Research Computing Program - 22 May 2014
Rasmus Nielsen - Berkeley Research Computing Program - 22 May 2014
::2014/06/10::
Play Video
49
DNA, quantum computers and Luke Skywalkers hand
DNA, quantum computers and Luke Skywalkers hand
::2013/08/05::
Play Video
50
Rebooting The Cosmos: Is the Universe The Ultimate Computer? (Full)
Rebooting The Cosmos: Is the Universe The Ultimate Computer? (Full)
::2012/04/16::
NEXT >>
RESULTS [51 .. 101]
From Wikipedia, the free encyclopedia
Jump to: navigation, search
For hypothetical computers using brain-to-brain interfaces see Biological computer

DNA computing is a form of computing which uses DNA, biochemistry and molecular biology, instead of the traditional silicon-based computer technologies. DNA computing, or, more generally, biomolecular computing, is a fast developing interdisciplinary area. Research and development in this area concerns theory, experiments, and applications of DNA computing. The term "molectronics" has sometimes been used, but this term had already been used for an earlier technology, a then-unsuccessful rival of the first integrated circuits;[1] this term has also been used more generally, for molecular-scale technology.[2]

History[edit]

This field was initially developed by Leonard Adleman of the University of Southern California, in 1994.[3] Adleman demonstrated a proof-of-concept use of DNA as a form of computation which solved the seven-point Hamiltonian path problem. Since the initial Adleman experiments, advances have been made and various Turing machines have been proven to be constructible.[4][5]

While the initial interest was in using this novel approach to tackle NP-hard problems, it was soon realized that they may not be best suited for this type of computation, and several proposals have been made to find a "killer application" for this approach. In 1997, computer scientist Mitsunori Ogihara working with biologist Animesh Ray suggested one to be the evaluation of Boolean circuits and described an implementation.[6][7]

In 2002, researchers from the Weizmann Institute of Science in Rehovot, Israel, unveiled a programmable molecular computing machine composed of enzymes and DNA molecules instead of silicon microchips.[8] On April 28, 2004, Ehud Shapiro, Yaakov Benenson, Binyamin Gil, Uri Ben-Dor, and Rivka Adar at the Weizmann Institute announced in the journal Nature that they had constructed a DNA computer coupled with an input and output module which would theoretically be capable of diagnosing cancerous activity within a cell, and releasing an anti-cancer drug upon diagnosis.[9]

In January 2013, researchers were able to store a JPEG photograph, a set of Shakespearean sonnets, and an audio file of Martin Luther King, Jr.'s speech I Have a Dream on DNA digital data storage.[10]

In March 2013, researchers created a transcriptor (a biological transistor).

Capabilities[edit]

DNA computing is a form of parallel computing in that it takes advantage of the many different molecules of DNA to try many different possibilities at once.[11] For certain specialized problems, DNA computers are faster and smaller than any other computer built so far. Furthermore, particular mathematical computations have been demonstrated to work on a DNA computer. As an example, DNA molecules have been utilized to tackle the assignment problem.[12] Aran Nayebi[13] has provided a general implementation of Strassen's matrix multiplication algorithm on a DNA computer, although there are problems with scaling. In addition, Caltech researchers have created a circuit made from 130 unique DNA strands, which is able to calculate the square root of numbers up to 15.[14]

DNA computing does not provide any new capabilities from the standpoint of computability theory, the study of which problems are computationally solvable using different models of computation. For example, if the space required for the solution of a problem grows exponentially with the size of the problem (EXPSPACE problems) on von Neumann machines, it still grows exponentially with the size of the problem on DNA machines. For very large EXPSPACE problems, the amount of DNA required is too large to be practical.

Methods[edit]

There are multiple methods for building a computing device based on DNA, each with its own advantages and disadvantages. Most of these build the basic logic gates (AND, OR, NOT) associated with digital logic from a DNA basis. Some of the different bases include DNAzymes, deoxyoligonucleotides, enzymes, DNA tiling, and polymerase chain reaction.

DNAzymes[edit]

Catalytic DNA (deoxyribozyme or DNAzyme) catalyze a reaction when interacting with the appropriate input, such as a matching oligonucleotide. These DNAzymes are used to build logic gates analogous to digital logic in silicon; however, DNAzymes are limited to 1-, 2-, and 3-input gates with no current implementation for evaluating statements in series.

The DNAzyme logic gate changes its structure when it binds to a matching oligonucleotide and the fluorogenic substrate it is bonded to is cleaved free. While other materials can be used, most models use a fluorescence-based substrate because it is very easy to detect, even at the single molecule limit.[15] The amount of fluorescence can then be measured to tell whether or not a reaction took place. The DNAzyme that changes is then “used,” and cannot initiate any more reactions. Because of this, these reactions take place in a device such as a continuous stirred-tank reactor, where old product is removed and new molecules added.

Two commonly used DNAzymes are named E6 and 8-17. These are popular because they allow cleaving of a substrate in any arbitrary location.[16] Stojanovic and MacDonald have used the E6 DNAzymes to build the MAYA I[17] and MAYA II[18] machines, respectively; Stojanovic has also demonstrated logic gates using the 8-17 DNAzyme.[19] While these DNAzymes have been demonstrated to be useful for constructing logic gates, they are limited by the need for a metal cofactor to function, such as Zn2+ or Mn2+, and thus are not useful in vivo.[15][20]

A design called a stem loop, consisting of a single strand of DNA which has a loop at an end, are a dynamic structure that opens and closes when a piece of DNA bonds to the loop part. This effect has been exploited to create several logic gates. These logic gates have been used to create the computers MAYA I and MAYA II which can play tic-tac-toe to some extent.[21]

Enzymes[edit]

Enzyme based DNA computers are usually of the form of a simple Turing machine; there is analogous hardware, in the form of an enzyme, and software, in the form of DNA.[22]

Benenson, Shapiro and colleagues have demonstrated a DNA computer using the FokI enzyme[23] and expanded on their work by going on to show automata that diagnose and react to prostate cancer: under expression of the genes PPAP2B and GSTP1 and an over expression of PIM1 and HPN.[9] Their automata evaluated the expression of each gene, one gene at a time, and on positive diagnosis then released a single strand DNA molecule (ssDNA) that is an antisense for MDM2. MDM2 is a repressor of protein 53, which itself is a tumor suppressor.[24] On negative diagnosis it was decided to release a suppressor of the positive diagnosis drug instead of doing nothing. A limitation of this implementation is that two separate automata are required, one to administer each drug. The entire process of evaluation until drug release took around an hour to complete. This method also requires transition molecules as well as the FokI enzyme to be present. The requirement for the FokI enzyme limits application in vivo, at least for use in “cells of higher organisms”.[25] It should also be pointed out that the 'software' molecules can be reused in this case.

Toehold exchange[edit]

DNA computers have also been constructed using the concept of toehold exchange. In this system, an input DNA strand binds to a sticky end, or toehold, on another DNA molecule, which allows it to displace another strand segment from the molecule. This allows the creation of modular logic components such as AND, OR, and NOT gates and signal amplifiers, which can be linked into arbitrarily large computers. This class of DNA computers does not require enzymes or any chemical capability of the DNA.[26]

Algorithmic self-assembly[edit]

DNA arrays that display a representation of the Sierpinski gasket on their surfaces. Click the image for further details. Image from Rothemund et al., 2004.[27]

DNA nanotechnology has been applied to the related field of DNA computing. DNA tiles can be designed to contain multiple sticky ends with sequences chosen so that they act as Wang tiles. A DX array has been demonstrated whose assembly encodes an XOR operation; this allows the DNA array to implement a cellular automaton which generates a fractal called the Sierpinski gasket. This shows that computation can be incorporated into the assembly of DNA arrays, increasing its scope beyond simple periodic arrays.[27]

See also[edit]

References[edit]

  1. ^ "Molectronic Computer Shown by Texas Instr.", unknown publication, circa 1963, in Box 2, Folder 3, listed in Jack Kilby Papers: A Guide to the Collection, Southern Methodist University. [1] .
  2. ^ "Application-specific methods for testing molectronic or nanoscale devices" (filed April 1,2004), Patent US 7219314 B1. [2] .
  3. ^ Adleman, L. M. (1994). "Molecular computation of solutions to combinatorial problems". Science 266 (5187): 1021–1024. doi:10.1126/science.7973651. PMID 7973651.  edit — The first DNA computing paper. Describes a solution for the directed Hamiltonian path problem. Also available here: [3]
  4. ^ Boneh, D.; Dunworth, C.; Lipton, R. J.; Sgall, J. Í. (1996). "On the computational power of DNA". Discrete Applied Mathematics 71: 79–94. doi:10.1016/S0166-218X(96)00058-3.  edit — Describes a solution for the boolean satisfiability problem. Also available here: [4]
  5. ^ Lila Kari, Greg Gloor, Sheng Yu (January 2000). "Using DNA to solve the Bounded Post Correspondence Problem". Theoretical Computer Science 231 (2): 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: [5]
  6. ^ M. Ogihara and A. Ray, "Simulating Boolean circuits on a DNA computer". Algorithmica 25:239–250, 1999.
  7. ^ "In Just a Few Drops, A Breakthrough in Computing", New York Times, May 21, 1997
  8. ^ Lovgren, Stefan (2003-02-24). "Computer Made from DNA and Enzymes". National Geographic. Retrieved 2009-11-26. 
  9. ^ a b Benenson, Y.; Gil, B.; Ben-Dor, U.; Adar, R.; Shapiro, E. (2004). "An autonomous molecular computer for logical control of gene expression". Nature 429 (6990): 423–429. doi:10.1038/nature02551. PMC 3838955. PMID 15116117.  edit. Also available here: [6]
  10. ^ [7]
  11. ^ Lewin, D. I. (2002). "DNA computing". Computing in Science & Engineering 4 (3): 5–8. doi:10.1109/5992.998634.  edit
  12. ^ Shu, Jian-Jun; Wang, Q.-W.; Yong, K.-Y. (2011). "DNA-based computing of strategic assignment problems". Physical Review Letters 106 (18): 188702. doi:10.1103/PhysRevLett.106.188702. 
  13. ^ Nayebi, Aran (2009). "Fast matrix multiplication techniques based on the Adleman-Lipton model". arXiv: 0912.0750: 1–13. 
  14. ^ Science NewsFlexbile DNA computer finds square roots
  15. ^ a b Weiss, S. (1999). "Fluorescence Spectroscopy of Single Biomolecules". Science 283 (5408): 1676–1683. doi:10.1126/science.283.5408.1676. PMID 10073925.  edit. Also available here: http://www.lps.ens.fr/~vincent/smb/PDF/weiss-1.pdf
  16. ^ Santoro, S. W.; Joyce, G. F. (1997). "A general purpose RNA-cleaving DNA enzyme". Proceedings of the National Academy of Sciences 94 (9): 4262–4266. doi:10.1073/pnas.94.9.4262.  edit. Also available here: [8]
  17. ^ Stojanovic, M. N.; Stefanovic, D. (2003). "A deoxyribozyme-based molecular automaton". Nature Biotechnology 21 (9): 1069–1074. doi:10.1038/nbt862. PMID 12923549.  edit. Also available here: [9]
  18. ^ MacDonald, J.; Li, Y.; Sutovic, M.; Lederman, H.; Pendri, K.; Lu, W.; Andrews, B. L.; Stefanovic, D.; Stojanovic, M. N. (2006). "Medium Scale Integration of Molecular Logic Gates in an Automaton". Nano Letters 6 (11): 2598–2603. doi:10.1021/nl0620684. PMID 17090098.  edit. Also available here: [10]
  19. ^ Stojanovic, M. N.; Mitchell, T. E.; Stefanovic, D. (2002). "Deoxyribozyme-Based Logic Gates". Journal of the American Chemical Society 124 (14): 3555–3561. doi:10.1021/ja016756v. PMID 11929243.  edit. Also available at [11]
  20. ^ Cruz, R. P. G.; Withers, J. B.; Li, Y. (2004). "Dinucleotide Junction Cleavage Versatility of 8-17 Deoxyribozyme". Chemistry & Biology 11: 57–67. doi:10.1016/j.chembiol.2003.12.012.  edit
  21. ^ Darko Stefanovic's Group, Molecular Logic Gates and MAYA II, a second-generation tic-tac-toe playing automaton.
  22. ^ Shapiro, Ehud (1999-12-07). "A Mechanical Turing Machine: Blueprint for a Biomolecular Computer". Weizmann Institute of Science. Retrieved 2009-08-13. 
  23. ^ Benenson, Y.; Paz-Elizur, T.; Adar, R.; Keinan, E.; Livneh, Z.; Shapiro, E. (2001). "Programmable and autonomous computing machine made of biomolecules". Nature 414 (6862): 430–434. doi:10.1038/35106533. PMID 11719800.  edit. Also available here: [12]
  24. ^ Bond, G. L.; Hu, W.; Levine, A. J. (2005). "MDM2 is a Central Node in the p53 Pathway: 12 Years and Counting". Current Cancer Drug Targets 5 (1): 3–8. doi:10.2174/1568009053332627. PMID 15720184.  edit
  25. ^ Kahan, M.; Gil, B.; Adar, R.; Shapiro, E. (2008). "Towards molecular computers that operate in a biological environment". Physica D: Nonlinear Phenomena 237 (9): 1165–1172. Bibcode:2008PhyD..237.1165K. doi:10.1016/j.physd.2008.01.027.  edit. Also available here: [13]
  26. ^ Seelig, G.; Soloveichik, D.; Zhang, D. Y.; Winfree, E. (8 December 2006). "Enzyme-free nucleic acid logic circuits". Science 314 (5805): 1585–1588. doi:10.1126/science.1132493. PMID 17158324.  edit
  27. ^ a b Rothemund, P. W. K.; Papadakis, N.; Winfree, E. (2004). "Algorithmic Self-Assembly of DNA Sierpinski Triangles". PLoS Biology 2 (12): e424. doi:10.1371/journal.pbio.0020424. PMC 534809. PMID 15583715.  edit

Further reading[edit]

Martyn Amos, Genesis Machines, popular science introduction to the field.

  • Martyn Amos (June 2005). Theoretical and Experimental DNA Computation. Springer. ISBN 3-540-65773-8.  — The first general text to cover the whole field.
  • Gheorge Paun, Grzegorz Rozenberg, Arto Salomaa (October 1998). DNA Computing - New Computing Paradigms. Springer-Verlag. ISBN 3-540-64196-3.  — The book starts with an introduction to DNA-related matters, the basics of biochemistry and language and computation theory, and progresses to the advanced mathematical theory of DNA computing.
  • JB. Waldner (January 2007). Nanocomputers and Swarm Intelligence. ISTE. p. 189. ISBN 2-7462-1516-0. 
  • Zoja Ignatova, Israel Martinez-Perez, Karl-Heinz Zimmermann (January 2008). DNA Computing Models. Springer. p. 288. ISBN 978-0-387-73635-8.  — A new general text to cover the whole field.

External links[edit]

Wikipedia content is licensed under the GFDL License
Powered by YouTube
LEGAL
  • Mashpedia © 2014