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Test Tube Selection of Large Independent Sets of DNA Oligonucleotides

  • Russell Deaton
  • Junghuei Chen
  • Jin-Woo Kim
  • Max H. Garzon
  • David H. Wood
Part of the Natural Computing Series book series (NCS)

7 Conclusion

Self-assembly of nanostructures through template-matching hybridization reactions is potentially an important technique in nanotechnology. Given the possibility of errors in hybridization and the difficulty of designing DNA sequences on conventional computers, a viable alternative is to manufacture libraries of oligonucleotides for nanotechnology applications in the test tube. Thus, a protocol has been designed and tested to select mismatched oligonucleotides from a random starting material. Experiments indicate that the selected oligonucleotides are independent, and that there are about 10 000 distinct sequences. Such manufactured libraries are a potential enabling resource for DNA self-assembly in nanotechnology.

Keywords

Selection Protocol Selection Product Duplex Formation Primer Extension Product Nucleation Rate Constant 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    L.M. Adleman, Molecular computation of solutions to combinatorial problems, Science, 266 (1994) 1021–1024.Google Scholar
  2. 2.
    A. Bachtold, P. Hadley, T. Nakanishi, C. Dekker, Logic circuits with carbon nanotube transistors, Science, 294 (2001) 1317–1320.CrossRefGoogle Scholar
  3. 3.
    H. Bi, J. Chen, R. Deaton, M. Garzon, H. Rubin, D.H. Wood, In Vitro selection for non-crosshybridizing oligonucleotides for computation, Natural Comput., 2 (2003) 417–426.MathSciNetCrossRefGoogle Scholar
  4. 4.
    V.A. Bloomfield, D.M. Crothers, I. Tinoco Jr., Nucleic Acids: Structures, Properties, and Functions, University Science Books, Sausalito, CA, 2000.Google Scholar
  5. 5.
    E. Braun, U. Sivan, DNA-templated electronics, Nanobiotechnology, C.M. Niemeyer, C.A. Mirkin eds., Wiley-VCH, Weinheim, (2004) 244–255.Google Scholar
  6. 6.
    R.J. Britten, D.E. Kohne, Repeated sequences in DNA, Science, 161 (1968) 529–540.Google Scholar
  7. 7.
    J. Charlton, D. Smith, Estimation of SELEX pool size by measurement of DNA renaturation rates, RNA, 5 (1999) 1326–1332.Google Scholar
  8. 8.
    J. Chen, R. Deaton, M. Garzon, J.W. Kim, D.H. Wood, H. Bi, D. Carpenter, Y.Z. Wang, Characterization of the non-crosshybridizing DNA oligonucleotides manufactured in vitro, DNA Computing: Preliminary Proceedings of the 10th International Workshop on DNA-Based Computers, G. Mauri, L. Smith eds., Lecture Notes in Computer Science 3384 University of Milano-Bicocca, Milan, (2004) 50–61.Google Scholar
  9. 9.
    J. Chen, R. Deaton, M. Garzon, J.W. Kim, D.H. Wood, H. Bi, D. Carpenter, J.S. Lee, Y.Z. Wang, Sequence complexity of large libraries of DNA oligonucleotides, DNA Computing: Preliminary Proceedings of the 11th International Workshop on DNA-Based Computers, N. Pierce, A. Carbone eds., University of Western Ontario, London, Ontario, Canada, 2005.Google Scholar
  10. 10.
    J. Chen, J. Reif, eds., DNA Computing: 9th International Workshop on DNABased Computers, Lecture Notes in Computer Science, 2943 Springer, Berlin, Heidelberg, 2004.Google Scholar
  11. 11.
    R. Deaton, M. Garzon, J.A. Rose, D.R. Franceschetti, R.C. Murphy, S.E. Stevens Jr., Reliability and efficiency of a DNA based computation, Phys. Rev. Lett., 80 (1998) 417–420.CrossRefGoogle Scholar
  12. 12.
    R. Deaton, J.W. Kim, J. Chen, Design and test of non-crosshybridizing oligonucleotide building blocks for DNA computers and nanostructures, Appl. Phys. Lett., 82 (2003) 1305–1307.CrossRefGoogle Scholar
  13. 13.
    R. Deaton, J. Chen, H. Bi, J.A. Rose, A software tool for generating noncrosshybridizing libraries of DNA oligonucleotides, DNA Computing: 8th International Workshop on DNA-Based Computers, M. Hagiya, A. Ohuchi eds., Lecture Notes in Computer Science, 2568 Springer, Berlin, Heidelberg, (2003) 252–261.Google Scholar
  14. 14.
    R. Deaton, J. Chen, H. Bi, M. Garzon, H. Rubin, D.H. Wood, A PCR-based protocol for in vitro selection of non-crosshybridizing oligonucleotides, DNA Computing: 8th International Workshop on DNA-Based Computers, M. Hagiya, A. Ohuchi eds., Lecture Notes in Computer Science, Springer, Berlin, Heidelberg, 2568 (2003) 196–204.Google Scholar
  15. 15.
    A.G. Frutos, Q. Liu, A.J. Thiel, A.M.W. Sanner, A.E. Condon, L.M. Smith, R.M. Corn, Demonstration of a word design strategy for DNA computing on surfaces, Nucleic Acids Res., 25 (1997) p. 4748.CrossRefGoogle Scholar
  16. 16.
    M.R. Garey, D.S. Johnson, Computers and Intractability, Freeman, New York, 1979.Google Scholar
  17. 17.
    M.H. Garzon, R.J. Deaton, Codeword design and information encoding in DNA ensembles, Natural Comput., 3 (2004) 253–292.MathSciNetCrossRefGoogle Scholar
  18. 18.
    M. Hagiya, A. Ohuchi, eds., DNA Computing: 8th International Workshop on DNA-Based Computers, Lecture Notes in Computer Science, 2568 Springer, 2003.Google Scholar
  19. 19.
    K. Keren, R.S. Berman, E. Buchstab, U. Sivan, E. Braun, DNA-templated carbon nanotube field-effect transistor, Science, 302 (2003) 1380–1382.CrossRefGoogle Scholar
  20. 20.
    A. Marathe, A.E. Condon, R.M. Corn, On combinatorial DNA word design, DNA Based Computers V, E. Winfree, D.K. Gifford, eds., Providence, RI, DIMACS, American Mathematical Society, (1999) 75–90.Google Scholar
  21. 21.
    G. Mauri, L. Smith, eds., DNA Computing: Preliminary Proceedings of the 10th International Workshop on DNA-Based Computers, Lecture Notes in Computer Science 3384, Springer, Berlin, Heidelberg, 2005.Google Scholar
  22. 22.
    C. Mirkin, R. L. Letsinger, R. C. Mucic, J. J. Storhoff, A DNA-based method for rationally assembling nanoparticles into macroscopic materials, Nature, 382 (1996) 607–609.CrossRefGoogle Scholar
  23. 23.
    C.M. Niemeyer, C.A. Mirkin, eds., Nanobiotechnology, Wiley-VCH, Weinheim, 2004.Google Scholar
  24. 24.
    J. SantaLucia Jr., A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proc. Natl. Acad. Sci. USA, 95 (1998) 1460–1465.CrossRefGoogle Scholar
  25. 25.
    N.C. Seeman, H. Wang, X. Yang, F. Liu, C. Mao, W. Sun, L. Wenzler, Z. Shen, R. Sha, H. Yan, M.H. Wong, P. Sa-Ardyen, B. Liu, H. Qiu, X. Li, J. Qi, S.M. Du, Y. Zhang, J.E. Mueller, T. Fu, Y. Wang, J. Chen, New motifs in DNA nanotechnology, Nanotechnology, 9 (1998) 257–273.CrossRefGoogle Scholar
  26. 26.
    N.C. Seeman, H. Wang, B. Liu, J. Qi, X. Li, X. Yang, F. Liu, W. Sun, Z. Shen, R. Sha, C. Mao, Y. Wang, S. Zhang, T. Fu, S. Du, J.E. Mueller, Y. Zhang, J. Chen, The perils of polynucleotides: the experimental gap between the design and assembly of unusual DNA structures, Proceedings of the Second Annual Meeting on DNA Based Computers L.F. Landweber, E.B. Baum eds., 44 PRovidence, Ri, DIMACS, American Mathematical Society, (1998) 191–205.Google Scholar
  27. 27.
    N.C. Seeman, DNA nanostructures for mechanics and computing: nonlinear thinking with life’s central molecule, Nanobiotechnology, C.M. Niemeyer, C.A. Mirkin eds., Wiley-VCH, Weinheim, (2004) 308–318.Google Scholar
  28. 28.
    C.S. Thaxton, C.A. Mirkin, DNA-gold nanoparticle conjugates, Nanobiotechnology, C.M. Niemeyer, C.A. Mirkin eds., Wiley-VCH, Weinheim, (2004) 288–307.Google Scholar
  29. 29.
    J.G. Wetmur, DNA probes: applications of the principle of nucleic acid hybridization, Crit. Rev. Biochem. Mol. Bio., 26 (1991) 227–259.Google Scholar
  30. 30.
    G.M. Whitesides, M. Boncheva, Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains, Proc. Natl. Acad. Sci. USA, 101 (2004) 11046–11051.CrossRefGoogle Scholar
  31. 31.
    G.M. Whitesides, M. Boncheva, Beyond molecules: self-assembly of mesoscopic and macroscopic components, Proc. Natl. Acad. Sci. USA, 99 (2002) 4769–4774.CrossRefGoogle Scholar
  32. 32.
    E. Winfree, F. Liu, L.A. Wenzler, N.C. Seeman, Design and self-assembly of two-dimensional DNA crystals, Nature, 394 (1998) 539–544.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Russell Deaton
    • 1
  • Junghuei Chen
    • 2
  • Jin-Woo Kim
    • 3
  • Max H. Garzon
    • 4
  • David H. Wood
    • 5
  1. 1.Computer Science and EngineeringUniversity of ArkansasFayettevilleUSA
  2. 2.Chemistry and BiochemistryUniversity of DelawareNewarkUSA
  3. 3.Biological EngineeringUniversity of ArkansasFayettevilleUSA
  4. 4.Computer ScienceUniversity of MemphisMemphisUSA
  5. 5.Computer and Information SciencesUniversity of DelawareNewarkUSA

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