Natural Computing

, Volume 5, Issue 2, pp 151–163 | Cite as

Application of Mismatch Detection Methods in DNA Computing

  • Christiaan V. Henkel
  • Grzegorz Rozenberg
  • Herman P. Spaink
Article
  • 57 Downloads

Abstract

In many implementations of DNA computing, reliable detection of hybridization is of prime importance. We have applied several well-established DNA mutation scanning methods to this problem. Since they have been developed for speed and accuracy, these technologies are very promising for DNA computing. We have benchmarked a heteroduplex migration assay and enzymatic detection of mismatches on a 4 variable instance of 3SAT, using a previously described blocking algorithm. The first method is promising, but yielded ambiguous results. On the other hand, we were able to distinguish all perfect from imperfect duplexes by means of a CEL I mismatch endonuclease assay.

Key words

DNA computing DNA hybridization mismatch detection mutation detection 

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References

  1. Braich, RS, Chelyapov, N, Johnson, C, Rothemund, PWK, Adleman, L 2002Solution of a 20-variable 3-SAT problem on a DNA computerScience296499502CrossRefGoogle Scholar
  2. Brown, J, Brown, T, Fox, KR 2001Affinity of mismatch-binding protein MutS for heteroduplexes containing different mismatchesBiochemical Journal354627633CrossRefGoogle Scholar
  3. Bui, CT, Rees, K, Lambrinakos, A, Bedir, A, Cotton, RGH 2002Site-selective reactions of imperfectly matched DNA with small chemical molecules: applications in mutation detectionBioorganic Chemistry30216232CrossRefGoogle Scholar
  4. Faulhammer, D, Cukras, AR, Lipton, RJ, Landweber, LF 2000Molecular computation: RNA solutions to chess problemsProceedings of the National Academy of Sciences of the United States of America9713851389CrossRefGoogle Scholar
  5. Ganguly, A, Rock, MJ, Prockop, DJ 1993Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: evidence for solvent-induced bends in DNA heteroduplexesProceedings of the National Academy of Sciences of the United States of America901032510329CrossRefGoogle Scholar
  6. Goode, E, Wood, DH, Chen, J 2001

    DNA implementation of a Royal Road fitness evaluation

    Condon, ARozenberg, G eds. DNA Computing, Proceedings 6th International Meeting on DNA Based ComputersSpringer-VerlagBerlin, Heidelberg247262
    Google Scholar
  7. Highsmith, WE, Jin, Q, Nataraj, AJ, O’Connor, JM, Burland, VD, Baubonis, WR, Curtis, FP, Kusukawa, N, Garner, MM 1999Use of a DNA toolbox for the characterization of mutation scanning methods. I: construction of the toolbox and evaluation of heteroduplex analysisElectrophoresis2011861194CrossRefGoogle Scholar
  8. Kristensen, VN, Kelefiotis, D, Kristensen, T, Borresen-Dale, AL 2001High-throughput methods for detection of genetic variationBiotechniques30318332Google Scholar
  9. Liu, QH, Wang, LM, Frutos, AG, Condon, AE, Corn, RM, Smith, LM 2000DNA computing on surfacesNature403175179CrossRefGoogle Scholar
  10. Loakes, D 2001The applications of universal DNA base analoguesNucleic Acids Research2924372447CrossRefGoogle Scholar
  11. Mashal, RD, Koontz, J, Sklar, J 1995Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvasesNature Genetics9177183CrossRefGoogle Scholar
  12. Nataraj, AJ, Olivos-Glander, I, Kusukawa, N, Highsmith, WE 1999Single-strand conformation polymorphism and heteroduplex analysis for gel-based mutation detectionElectrophoresis2011771185CrossRefGoogle Scholar
  13. Oleykowski, CA, Bronson Mullins, CR, Godwin, AK, Yeung, AT 1998Mutation detection using a novel plant endonucleaseNucleic Acids Research2645974602CrossRefGoogle Scholar
  14. Peyret, N, Seneviratne, PA, Allawi, HT, SantaLucia, J 1999Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A–A, C–C, G–G, and T–T mismatchesBiochemistry3834683477CrossRefGoogle Scholar
  15. Rozenberg, G, Spaink, H 2003DNA computing by blockingTheoretical Computer Science292653665MathSciNetCrossRefGoogle Scholar
  16. SantaLucia, J 1998A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamicsProceedings of the National Academy of Sciences of the United States of America9514601465CrossRefGoogle Scholar
  17. Schmidt, KA, Henkel, CV, Rozenberg, G, Spaink, HP 2002

    Experimental aspects of DNA computing by blocking: use of fluorescence techniques for detection

    Kraayenhof, RVisser, AJWGGerritsen, HC eds. Fluorescence Spectroscopy, Imaging and Probes – New Tools in Chemical, Physical and Life ScienceSpringer-VerlagBerlin, Heidelberg123128
    Google Scholar
  18. Schmidt, KA, Henkel, CV, Rozenberg, G, Spaink, HP 2004DNA computing using single-molecule hybridization detectionNucleic Acids Research3249624968CrossRefGoogle Scholar
  19. Taylor, GR 1999Enzymatic and chemical cleavage methodsElectrophoresis2011251130CrossRefGoogle Scholar
  20. Upchurch, DA, Shankarappa, R, Mullins, JI 2000Position and degree of mismatches and the mobility of DNA heteroduplexesNucleic Acids Research28e69CrossRefGoogle Scholar
  21. Wood, D, Chen, J, Antipov, E, Lemieux, B, Cedeno, W 1999

    A DNA implementation of the Max 1s problem

    Banzhaf, WEiben, AEGarzon, MHHonavar, VJakiela, MSmith, RE eds. Proceeding of the Genetic and Evolutionary Computation Conference 1999Morgan KaufmanSan Francisco18351841
    Google Scholar
  22. Yang, B, Wen, X, Kodali, NS, Oleykowski, CA, Miller, CG, Kulinski, J, Besack, D, Yeung, JA, Kowalski, D, Yeung, AT 2000Purification, cloning, and characterization of the CEL I nucleaseBiochemistry3935333541CrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • Christiaan V. Henkel
    • 1
    • 2
  • Grzegorz Rozenberg
    • 2
  • Herman P. Spaink
    • 1
  1. 1.Institute of BiologyLeiden UniversityLeidenThe Netherlands
  2. 2.Leiden Institute of Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands

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