Advertisement

Designing Nucleotide Sequences for Computation: A Survey of Constraints

  • Jennifer Sager
  • Darko Stefanovic
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)

Abstract

We survey common biochemical constraints useful for the design of DNA code words for DNA computation. We define the DNA Code Constraint Problem and cover biochemistry topics relevant to DNA libraries. We examine which biochemical constraints are best suited for DNA word design.

Keywords

Free Energy Secondary Structure Minimum Free Energy Hairpin Loop Bulge Loop 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular computation: RNA solutions to chess problems. Proceedings of the National Academy of Sciences of the USA (PNAS) 97(4), 1385–1389 (2000); The PERMUTE Program is available at: http://www.pnas.org/cgi/content/full/97/4/1385/DC1 CrossRefGoogle Scholar
  2. 2.
    Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266(5187), 1021–1024 (1994)CrossRefGoogle Scholar
  3. 3.
    Lipton, R.J.: DNA solution of hard computational problems. Science 268, 542–545 (1995)CrossRefGoogle Scholar
  4. 4.
    Deaton, R.J., Murphy, R.C., Garzon, M., Franceschetti, D.R., Stevens Jr., S.E.: Good encodings for DNA-based solutions to combinatorial problems. In: Landweber, Baum (eds.) [62], pp. 247–258Google Scholar
  5. 5.
    Brenneman, A., Condon, A.E.: Strand design for bio-molecular computation. Technical report, University of British Columbia (March 2001)Google Scholar
  6. 6.
    Mauri, G., Ferretti, C.: Word design for molecular computing: A survey. In: Chen, J., Reif, J.H. (eds.) DAN 2003. LNCS, vol. 2943, pp. 37–47. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  7. 7.
    Dirks, R.M., Lin, M., Winfree, E., Pierce, N.A.: Paradigms for computational nucleic acid design. Nucleic Acids Research 32(4), 1392–1403 (2004)CrossRefGoogle Scholar
  8. 8.
    Stojanovic, M.N., Stefanovic, D.: A deoxyribozyme-based molecular automaton. Nature Biotechnology 21(9), 1069–1074 (2003)CrossRefGoogle Scholar
  9. 9.
    Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31(13), 3406–3415 (2003), Mfold is available at: http://www.bioinfo.rpi.edu/applications/mfold CrossRefGoogle Scholar
  10. 10.
    SantaLucia Jr., J.: A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proceedings of the National Academy of Sciences of the USA (PNAS) 95, 1460–1465 (1998)CrossRefGoogle Scholar
  11. 11.
    Peyret, N.: Prediction of Nucleic Acid Hybridization: Parameters and Algorithms. PhD thesis, Wayne State University, Dept. of Chemistry (2000)Google Scholar
  12. 12.
    Seeman, N.C.: De Novo design of sequences for nucleic acid structural engineering. Journal of Biomolecular Structure & Dynamics 8(3), 573–581 (1990)CrossRefGoogle Scholar
  13. 13.
    Feldkamp, U., Rauhe, H., Banzhaf, W.: Software tools for DNA sequence design. Genetic Programming and Evolvable Machines 4(2), 153–171 (2003)CrossRefGoogle Scholar
  14. 14.
    Tanaka, F., Kameda, A., Yamamoto, M., Ohuchi, A.: Specificity of hybridization between DNA sequences based on free energy. In: Carbone, et al. (eds.) [63], pp. 366–375Google Scholar
  15. 15.
    Sen, D., Gilbert, W.: Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334(6180), 364–366 (1988)CrossRefGoogle Scholar
  16. 16.
    Seeman, N.C.: It started with Watson and Crick, but it sure didn’t end there: Pitfalls and possibilities beyond the classic double helix. Natural Computing: An international journal 1(1), 53–84 (2002)MathSciNetCrossRefMATHGoogle Scholar
  17. 17.
    Mir, K.U.: A restricted genetic alphabet for DNA computing. In: Landweber, Baum (eds.) [62]Google Scholar
  18. 18.
    Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9(1), 133–148 (1981)CrossRefGoogle Scholar
  19. 19.
    Andronescu, M., Dees, D., Slaybaugh, L., Zhao, Y., Condon, A., Cohen, B., Skiena, S.: Algorithms for testing that sets of DNA word designs avoid unwanted secondary structure. In: Hagiy, Ohuchi (eds.) [64], pp.182–195Google Scholar
  20. 20.
    Kobayashi, S.: Testing structure freeness of regular sets of biomolecular sequences. In: Ferretti, et al. (eds.) [65], pp. 395–404Google Scholar
  21. 21.
    Kijima, A., Kobayashi, S.: Efficient algorithm for testing structure freeness of finite set of biomolecular sequences. In: Carbone, et al. (eds.) [63], pp. 278–288Google Scholar
  22. 22.
    McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29(6-7), 1105–1119 (1990)CrossRefGoogle Scholar
  23. 23.
    Dirks, R.M., Pierce, N.A.: A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry 24(13), 1664–1677 (2003), NUPACK is available at: http://www.acm.caltech.edu/~niles/software.html CrossRefGoogle Scholar
  24. 24.
    Marathe, A., Condon, A.E., Corn, R.M.: On combinatorial DNA word design. Journal of Computational Biology 8(3), 201–220 (2001)CrossRefMATHGoogle Scholar
  25. 25.
    Leupold, P.: Partial words for DNA coding. In: Ferretti, et al. (eds.) [65]Google Scholar
  26. 26.
    Garzon, M., Neathery, P., Deaton, R.J., Murphy, R.C., Franceschetti, D.R., Stevens Jr., S.E.: A new metric for DNA computing. In: Proceedings 2nd Genetic Programming Conference, pp. 472–478 (1997)Google Scholar
  27. 27.
    Penchovsky, R., Ackermann, J.: DNA library design for molecular computation. Journal of Computational Biology 10(2), 215–229 (2003)CrossRefGoogle Scholar
  28. 28.
    D’yachkov, A.G., Macula, A.J., Pogozelski, W.K., Renz, T.E., Rykov, V.V., Torney, D.C.: A weighted insertion-deletion stacked pair thermodynamic metric. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA 2004. LNCS, vol. 3384, pp. 90–103. Springer, Heidelberg (2005); SynDCode is available at: http://cluster.ds.geneseo.edu:8080/ParallelDNA/ CrossRefGoogle Scholar
  29. 29.
    Dimitrov, R.A., Zuker, M.: Prediction of hybridization and melting for double-stranded nucleic acids. Biophysical Journal 87, 215–226 (2004)CrossRefGoogle Scholar
  30. 30.
    Rose, J.A., Deaton, R.J., Franceschetti, D.R., Garzon, M., Stevens Jr., S.E.: A statistical mechanical treatment of error in the annealing biostep of DNA computation. In: Special program in GECCO 1999, pp. 1829–1834 (June 1999)Google Scholar
  31. 31.
    Rose, J.A., Deaton, R.J.: The fidelity of annealing-ligation: A theoretical analysis. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, p. 231. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  32. 32.
    Rose, J.A., Deaton, R.J., Hayiya, M., Suyama, A.: The fidelity of the tag-antitag system. In: Jonoska, Seeman (eds.) [66]Google Scholar
  33. 33.
    Rose, J.A., Deaton, R.J., Hagiya, M., Suyama, A.: An equilibrium analysis of the efficiency of an autonomous molecular computer. Physical Review E 65(021910) (2002)Google Scholar
  34. 34.
    Rose, J.A., Hagiya, M., Suyama, A.: The fidelity of the tag-antitag system II: Reconcilation with the stringency picture. In: Proceedings of the Congress on Evolutionary Computation, p. 2749 (2003), NucleicPark is available at: http://hagi.is.s.u-tokyo.ac.jp/johnrose/
  35. 35.
    Rose, J.A., Deaton, R.J., Franceschetti, D.R., Garzon, M., Stevens Jr, S.E.: Hybridization error for DNA mixtures of N species (1999), http://engronline.ee.memphis.edu/molec/Misc/ci.pdf
  36. 36.
    Rose, J.A., Suyama, A.: Physical modeling of biomolecular computers: Models, limitations, and experimental validation. Natural Computing 3(4), 411–426 (2004)MathSciNetCrossRefGoogle Scholar
  37. 37.
    SantaLucia Jr., J., Hicks, D.: The thermodynamics of DNA structural motifs. Annual Review of Biophysics Biomolecular Structure 33, 415–440 (2004)CrossRefGoogle Scholar
  38. 38.
    Hartemink, A.J., Gifford, D.K.: Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. In: Rubin, H., Wood, D.H. (eds.) Preliminary Proceedings of DNA Based Computers III, DIMACS Workshop 1997, Philadelphia, PA, pp. 15–25. University of Pennsylvania (1997)Google Scholar
  39. 39.
    Alexander, J., Hartemink, D.K., Khodor, J.: Automated constraint-based nucleotide sequence selection for DNA computation. In: Kari, L., Rubin, H., Wood, D.H. (eds.) DNA Based Computers IV, DIMACS Workshop 1998, University of Pennsylvania: Philadelphia, PA, October (1999), Biosystems vol. 52(1-3), pp. 227–235. Elsevier, Amsterdam (1999)Google Scholar
  40. 40.
    Nishikawa, A., Yamamura, M., Hagiya, M.: DNA computation simulator based on abstract bases. Soft Computing 5(1), 25–38 (2001)CrossRefMATHGoogle Scholar
  41. 41.
    Mathews, D.H., Turner, D.H.: Dynalign: An algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology 317(217), 191–203 (2002)CrossRefGoogle Scholar
  42. 42.
    Dirks, R.M., Pierce, N.A.: An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Journal of Computational Chemistry 25, 1295–1304 (2004)CrossRefGoogle Scholar
  43. 43.
    Andronescu, M., Aguirre-Hernandez, R., Condon, A., Hoos, H.H.: RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Research 31(13), 3416–3422 (2003); RNAsoft is available at: http://www.rnasoft.ca/ CrossRefGoogle Scholar
  44. 44.
    Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zucker, M., Turner, D.H.: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the USA (PNAS) 101(19), 7287–7292 (2004); The free energy nearest neighbor parameters are available at: http://rna.chem.rochester.edu/, RNAstructure is available at: http://128.151.176.70/RNAstructure.html CrossRefGoogle Scholar
  45. 45.
    Hofacker, I.L.: Vienna RNA secondary structure server. Nucleic Acids Research 31(13), 3429–3431 (2003); Vienna Package is available at: http://www.tbi.univie.ac.at/~ivo/RNA/ CrossRefGoogle Scholar
  46. 46.
    Peyret, N., Saro, P., SantaLucia Jr, J.: HyTher server. HyTher Version 1.0 is available at: http://ozone2.chem.wayne.edu/
  47. 47.
    Peyret, N., Seneviratne, P.A., Allawi, H.T., John, S.J.: Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A-A, C-C, G-G, and T-T mismatches. Biochemistry 38, 3468–3477 (1999)CrossRefGoogle Scholar
  48. 48.
    Le Novère, N.: MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 17(12), 1226–1227 (2001); Melting is available at: http://www.ebi.ac.uk/~lenov/meltinghome.html CrossRefGoogle Scholar
  49. 49.
    Blake, R.D., Bizzaro, J.W., Blake, J.D., Day, G.R., Delcourt, S.G., Knowles, J., Marx, K.A., SantaLucia Jr., J.: Statistical mechanical simulation of polymeric DNA melting with MELTSIM. Bioinformatics 15(5), 370–375 (1999)CrossRefGoogle Scholar
  50. 50.
    MeltWin. MeltWin is available at: http://www.meltwin.com/
  51. 51.
    Flamm, C., Fontana, W., Hofacker, I.L., Schuster, P.: RNA folding at elementary step resolution. RNA 6, 325–338 (2000); Kinfold is available at: http://www.tbi.univie.ac.at/~xtof/RNA/Kinfold/ CrossRefGoogle Scholar
  52. 52.
    Garzon, M., Deaton, R.J., Rose, J.A., Lu, L., Franceschetti, D.R.: Soft molecular computing. In: Proc. DNA5-99 Workshop. AMS DIMACS Series in Theoretical Computer Science, vol. 54, pp. 91–100 (2000); EdnaCo is available at: http://zorro.cs.memphis.edu/~cswebadm/csweb/research/pages/bmc/
  53. 53.
    Visual OMP (Oligonucleotide Modeling Platform), DNA Software, Inc. Visual OMP is available at: http://www.dnasoftware.com
  54. 54.
    The DNA and Natural Algorithms Group. DNA design toolbox. DNA Design Toolbox is available at: http://www.dna.caltech.edu/DNAdesign/
  55. 55.
    Kim, D., Soo-Yong, S., In-Hee, L., Byoung-Tak, Z.: NACST/Seq: A sequence design system with multiobjective optimization. In: Hagiya, Ohuchi [64], pp. 242–251Google Scholar
  56. 56.
    Ruben, A.J., Freeland, S.J., Landweber, L.F.: PUNCH: An evolutionary algorithm for optimizing bit set selection. In: Jonoska, Seeman (eds.) [66], pp. 150–160Google Scholar
  57. 57.
    Bishop, M., Macula, A.J., Pogozelski, W.K., Renz, T.E., Rykov, V.V.: SynDCode: Cooperative DNA code generating software. In: Carbone, et al. (eds.) [63], p. 391Google Scholar
  58. 58.
    Pogozelski, W.K., Bernard, M.P., Priore, S.F., Macula, A.J.: Experimental validation of DNA sequences for DNA computing: Use of a SYBR green assay. In: Carbo, et al. (eds.) [63], pp. 322–331Google Scholar
  59. 59.
    Yin, P., Guo, B., Belmore, C., Palmeri, W., Winfree, E., LaBean, T.H., Reif, J.H.: Tilesoft: Sequence optimization software for designing DNA secondary structures (January 2004), http://www.cs.duke.edu/~reif/paper/peng/TileSoft/TileSoft.pdf
  60. 60.
    Deaton, R.J., Garzon, M.: Thermodynamic constraints on DNA-based computing. In: Păun, G. (ed.) Computing with Bio-Molecules, pp. 138–152. Springer, Singapore (1998)Google Scholar
  61. 61.
    Smith, W.D.: DNA computers in vitro and vivo. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers, DIMACS Workshop 1995. American Mathematical Society. Series in Discrete Mathematics and Theoretical Computer Science, vol. 27, pp. 121–185. Princeton University, Princeton, NJ (1996)Google Scholar
  62. 62.
    Landweber, L.F., Baum, E.B. (eds.): DNA Based Computers II, DIMACS Workshop 1996 (Princeton University: Princeton, NJ). Series in Discrete Mathematics and Theoretical Computer Science, vol. 44. American Mathematical Society (1999)Google Scholar
  63. 63.
    Carbone, A., Daley, M., Kari, L., McQuillan, I., Pierce, N. (eds.): DNA 2005. LNCS, vol. 3892. Springer, Heidelberg (2006)MATHGoogle Scholar
  64. 64.
    Hagiya, M., Ohuchi, A. (eds.): DNA 2002. LNCS, vol. 2568. Springer, Heidelberg (2003)MATHGoogle Scholar
  65. 65.
    Ferretti, C., Mauri, G., Zandron, C. (eds.): DNA 2004. LNCS, vol. 3384. Springer, Heidelberg (2005)Google Scholar
  66. 66.
    Jonoska, N., Seeman, N.C. (eds.): DNA 2001. LNCS, vol. 2340. Springer, Heidelberg (2002)MATHGoogle Scholar
  67. 67.
    Schuster, P.: Counting and maximum matching of RNA structures (preprint, January 2004) (accessed, 2/1/2005), http://www.tbi.univie.ac.at/~pks
  68. 68.
    Watson, J.D., Hopkins, N.H., Roberts, J.W., Steitz, J.A., Weiner, A.M.: Molecular Biology of the Gene, 4th edn. Benjamin/Cummings, Menlo Park, CA (1988)Google Scholar
  69. 69.
    Kubota, M., Hagiya, M.: Minimum basin algorithm: An effective analysis technique for DNA energy landscapes. In: Ferretti, et al. (eds.) [65], pp. 202–213Google Scholar
  70. 70.
    Tinoco Jr., I., Sauer, K., Wang, J.C., Puglisi, J.D.: Physical Chemistry: Principles and Applications in Biological Sciences, 4th edn. Prentice Hall, Englewood Cliffs (2002)Google Scholar
  71. 71.
    Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular Biology of the Cell, 4th edn. Garland, New York (2002)Google Scholar
  72. 72.
    Schuster, P., Stadler, P.F., Renner, A.: RNA structures and folding: From conventional to new issues in structure predictions. Current Opinion in Structural Biology 7(2), 229–235 (1997)CrossRefGoogle Scholar
  73. 73.
    Turner, D.H., Sugimoto, N., Freier, S.M.: RNA structure prediction. Annual Review of Biophysics and Biophysical Chemistry 17, 167–192 (1988)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Jennifer Sager
    • 1
  • Darko Stefanovic
    • 1
  1. 1.Department of Computer ScienceUniversity of New MexicoAlbuquerqueUSA

Personalised recommendations