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DNA運算

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生物兼容计算设备: 脱氧核糖核酸(DNA)

DNA计算DNA computing,或譯DNA運算)是一个新出現的交叉學門領域,利用DNA生物化学以及分子生物学原理,而非传统上以為基礎的电子计算技術。该领域涉及DNA计算的理论、实验和应用。虽然该领域最初始于 1994 年Len Adleman的计算应用演示,但现在已扩展到存储技术开发等其他几个方面、[1][2][3]纳米级成像模式、[4][5][6]合成控制器与反应网络、[7][8][9][10]等。

历史

DNA运算最先由南加州大学伦纳德·阿德曼在1994年实现。[11]Adleman演示了一种将DNA应用于解决七点 哈密頓路徑問題概念验证方法。自Adleman的实验以后,学界又取得了许多进展,多种图灵机被证明是可行的。[12] [13]

尽管一开始的研究热点集中在解决P/NP问题,但人们旋即意识到此类问题并不是DNA运算的最佳应用场合,以致有多种意见要求寻找杀手级应用。1997年,计算机学家 Mitsunori Ogihara和生物学家Animesh Ray一道提出了一种组合逻辑电路的评价方法,并描绘了实现方法。[14][15] 2002年,来自Weizmann Institute of Science的研究者公开了一种由DNA分子和酶,而不是硅组成的计算机器。[16] 2004年3月28日,Weizmann Institute的Ehud Shapiro, Yaakov Benenson, Binyamin Gil, Uri Ben-Dor,和Rivka Adar在自然杂志上发表文章称,他们实现了一种整合了输入输出的DNA计算机,理论上可以实现细胞内的癌症诊断,并释放抗癌药物。DNA分子由四种碱基组成,通过酶改变他们的排列可以进行计算。[17][18] 2004年,英国科学家成功的在一小团DNA中存储了大量文件,并成功读取。[19]

2003 年,Reif's group 首次展示了一种基于 DNA 的行走器,这种行走器可以沿着类似于线性跟随机器人的轨道行走。他们利用分子生物学作为行走器的能量来源。自首次展示以来,已经有多种基于 DNA 的步行器被展示出来。

优点和缺点

DNA 计算机的处理速度较慢(响应时间以分钟、小时或天计算,而不是以毫秒计算),但它可以进行大量的多重并行计算。这使得系统进行复杂计算所需的时间与进行简单计算所需的时间相近。之所以能做到这一点,是因为数百万或数十亿分子能同时相互影响。不过,分析 DNA 计算机给出的答案要比数字计算机难得多。

参见

外部連結

  1. ^ Church, G. M.; Gao, Y.; Kosuri, S. Next-Generation Digital Information Storage in DNA. Science. 2012-08-16, 337 (6102): 1628. Bibcode:2012Sci...337.1628C. ISSN 0036-8075. PMID 22903519. S2CID 934617. doi:10.1126/science.1226355可免费查阅. 
  2. ^ Erlich, Yaniv; Zielinski, Dina. DNA Fountain enables a robust and efficient storage architecture. Science. 2017-03-02, 355 (6328): 950–954 [2024-01-17]. Bibcode:2017Sci...355..950E. ISSN 0036-8075. PMID 28254941. S2CID 13470340. doi:10.1126/science.aaj2038. (原始内容存档于2023-03-06). 
  3. ^ Organick, Lee; Ang, Siena Dumas; Chen, Yuan-Jyue; Lopez, Randolph; Yekhanin, Sergey; Makarychev, Konstantin; Racz, Miklos Z.; Kamath, Govinda; Gopalan, Parikshit; Nguyen, Bichlien; Takahashi, Christopher N. Random access in large-scale DNA data storage. Nature Biotechnology. March 2018, 36 (3): 242–248 [2024-01-17]. ISSN 1546-1696. PMID 29457795. S2CID 205285821. doi:10.1038/nbt.4079. (原始内容存档于2024-03-27) (英语). 
  4. ^ Shah, Shalin; Dubey, Abhishek K.; Reif, John. Programming Temporal DNA Barcodes for Single-Molecule Fingerprinting. Nano Letters. 2019-04-10, 19 (4): 2668–2673. Bibcode:2019NanoL..19.2668S. ISSN 1530-6984. PMID 30896178. S2CID 84841635. doi:10.1021/acs.nanolett.9b00590. 
  5. ^ Sharonov, Alexey; Hochstrasser, Robin M. Wide-field subdiffraction imaging by accumulated binding of diffusing probes. Proceedings of the National Academy of Sciences. 2006-12-12, 103 (50): 18911–18916. Bibcode:2006PNAS..10318911S. ISSN 0027-8424. PMC 1748151可免费查阅. PMID 17142314. doi:10.1073/pnas.0609643104可免费查阅 (英语). 
  6. ^ Jungmann, Ralf; Avendaño, Maier S.; Dai, Mingjie; Woehrstein, Johannes B.; Agasti, Sarit S.; Feiger, Zachary; Rodal, Avital; Yin, Peng. Quantitative super-resolution imaging with qPAINT. Nature Methods. May 2016, 13 (5): 439–442. ISSN 1548-7105. PMC 4941813可免费查阅. PMID 27018580. doi:10.1038/nmeth.3804 (英语). 
  7. ^ Shah, Shalin; Wee, Jasmine; Song, Tianqi; Ceze, Luis; Strauss, Karin; Chen, Yuan-Jyue; Reif, John. Using Strand Displacing Polymerase To Program Chemical Reaction Networks. Journal of the American Chemical Society. 2020-05-04, 142 (21): 9587–9593. ISSN 0002-7863. PMID 32364723. S2CID 218504535. doi:10.1021/jacs.0c02240. 
  8. ^ Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg. Programmable chemical controllers made from DNA. Nature Nanotechnology. October 2013, 8 (10): 755–762. Bibcode:2013NatNa...8..755C. ISSN 1748-3395. PMC 4150546可免费查阅. PMID 24077029. doi:10.1038/nnano.2013.189 (英语). 
  9. ^ Srinivas, Niranjan; Parkin, James; Seelig, Georg; Winfree, Erik; Soloveichik, David. Enzyme-free nucleic acid dynamical systems. Science. 2017-12-15, 358 (6369): eaal2052. ISSN 0036-8075. PMID 29242317. doi:10.1126/science.aal2052可免费查阅 (英语). 
  10. ^ Soloveichik, David; Seelig, Georg; Winfree, Erik. DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences. 2010-03-23, 107 (12): 5393–5398. Bibcode:2010PNAS..107.5393S. ISSN 0027-8424. PMC 2851759可免费查阅. PMID 20203007. doi:10.1073/pnas.0909380107可免费查阅 (英语). 
  11. ^ L. M. Adleman. Molecular computation of solutions to combinatorial problems. Science. 1994-11-11, 266 (5187): 1021–1024 [2018-04-02]. ISSN 0036-8075. doi:10.1126/science.7973651. (原始内容存档于2018-01-31) (英语).  — 第一篇DNA运算文章.描述分立的 哈密頓路徑問題.参阅: 存档副本 (PDF). [2005-11-21]. (原始内容 (PDF)存档于2005-02-06). 
  12. ^ Dan Boneh, Christopher Dunworth, Richard J. Lipton, Jir̆í Sgall. On the computational power of DNA. Discrete Applied Mathematics: 79–94. [2018-04-02]. doi:10.1016/s0166-218x(96)00058-3. (原始内容存档于2018-06-04).  — 描述布尔可满足性问题.参阅: 存档副本 (PDF). [2011-10-14]. (原始内容 (PDF)存档于2012-04-06). 
  13. ^ Lila Kari, Greg Gloor, Sheng Yu. Using DNA to solve the Bounded Post Correspondence Problem. Theoretical Computer Science. January 2000, 231 (2): 192–203 [2011-10-22]. (原始内容存档于2008-04-18). 参阅: http://www.csd.uwo.ca/~lila/pdfs/Using%20DNA%20to%20solve%20the%20Bounded%20Post%20Correspondence%20Problem.pdf页面存档备份,存于互联网档案馆
  14. ^ M. Ogihara and A. Ray, "Simulating Boolean circuits on a DNA computer"页面存档备份,存于互联网档案馆). Algorithmica 25:239–250, 1999.
  15. ^ "In Just a Few Drops, A Breakthrough in Computing"页面存档备份,存于互联网档案馆), 纽约时报, May 21, 1997
  16. ^ Lovgren, Stefan. Computer Made from DNA and Enzymes. National Geographic. 2003-02-24 [2009-11-26]. (原始内容存档于2003-02-26). 
  17. ^ Shu, Jian-Jun; Wang, Q.-W.; Yong, K.-Y. DNA-based computing of strategic assignment problems. Physical Review Letters. 3 May 2011, 106 (18): 188702. Bibcode:2011PhRvL.106r8702S. PMID 21635133. S2CID 25989989. doi:10.1103/PhysRevLett.106.188702. 
  18. ^ Shu, Jian-Jun; Wang, Q.-W.; Yong, K.-Y.; Shao, F.; Lee, K.J. Programmable DNA-mediated multitasking processor. Journal of Physical Chemistry B. 30 April 2015, 119 (17): 5639–5644. Bibcode:2015arXiv150803509S. PMID 25874653. S2CID 10446710. arXiv:1508.03509可免费查阅. doi:10.1021/acs.jpcb.5b02165. 
  19. ^ Yaakov Benenson, Binyamin Gil, Uri Ben-Dor, Rivka Adar, Ehud Shapiro. An autonomous molecular computer for logical control of gene expression. Nature. 2004/05, 429 (6990): 423–429 [2018-04-02]. ISSN 1476-4687. doi:10.1038/nature02551. (原始内容存档于2019-02-15) (英语).  . Also aviable here: 存档副本 (PDF). [2013-10-23]. (原始内容 (PDF)存档于2012-04-02). 
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DNA運算
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