Evaluating polynomials on the molecular level - A novel approach to molecular computers

BioSystems

Volumn 45, Issue 1, 1998, Pages 45-57

  Kulić, Igor M ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

DNA supercoil transfer; DNA topology; DNA based computing; Molecular computer

Indexed keywords

ARTICLE; COMPUTER; DNA STRUCTURE; ENERGY TRANSFER; GENE CONTROL; GENOME; MOLECULAR BIOLOGY;

EID: 0031983463     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(97)00060-9     Document Type: Article

References (33)

1. Adleman L.M. Molecular computation of solutions to combinatorial problems. Science. 266:1994;1021-1024.
2. Adleman, L.M., 1996. On constructing a molecular computer. Preprint. ftp://usc.edu/pub/csinfo/papers/adleman/molecular computer.ps.
3. Adleman, L.M., Rothemund, P.W.K., Roweis, S., Winfee, E., 1996. On applying molecular computation to the data encryption standard. Proceedings of the 2nd Annual Meeting on DNA Based Computers, Princeton University, 10-12 June, 1996. DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, ISSN 1052-1789, 1996.
4. Boneh, D., Dunworth, C., Lipton, R.J., 1995a. Breaking DES using a molecular computer. Technical Report CS-TR-48995, Princeton University.
5. Boneh, D., Dunworth, C., Sgall, J., 1995b. On computational power of DNA. Technical Report TR499-95, Princeton University, October.
6. Beaver D. Computing with DNA. J. Comput. Biol. 2(1):1995;1-8.
7. Beaver, D., 1995b. Molecular computing. Technical Report TR95-001, Pennsylvania State University, 31 January.
8. Cai, W., Condon, A.E., Corn, R.M., Glaser, E., Fei, Z., Frutos, T., Guo, Z., Lagally, M.G., Liu, Q., Smith, L.M., Thiel, A., 1996. The power of surface-based DNA computation. Preprint. ftp://corninfo.chem.wisc.edu/Papers/powerDNA.ps.
9. Csuhaj-Varju, E., Freund, R., Kari, L., Paun, G., 1996a. DNA computation based on splicing: universality results. Technical Report 185-2/FR2/95, TU Wien, Institute for Computer Languages, Wien, Austria, 1995.
10. Csuhaj-Varju E., Kari L., Paun G. Test tube distributed systems based on splicing. Comput. AI. 15(2-3):1996;211-232.
11. Dröge P., Nordheim A. Transcription-induced conformational change in a topologically closed DNA domain. Nucleic Acids Res. 19(11):1991;2941-2946.
12. Dröge P., Pohl F.M. The influence of an alternative template conformation on elongating phage T7 RNA polymerase. Nucleic Acids Res. 19(19):1991;5301-5306.
13. Dröge P. Protein tracking-induced supercoiling of DNA: a tool to regulate DNA transactions in vivo? BioEssays. 16(2):1993;91-99.
14. Dröge P. Transcription-driven site-specific DNA recombination in vitro. Proc. Natl. Acad. Sci. USA. 90:1993;2759-2763.
15. Ellison M.J., Fenton M.J., Ho P.S., Rich A. Long range interactions of multiple DNA structural transitions within a common topological domain. EMBO J. 6(5):1987;1513-1522.
16. Kanaar R., van de Putte P. Topological aspects of site-specific DNA-inversion. BioEssays. 7(5):1987;195-200.
17. Kelleher R.J., Ellison M.J., Ho P.S., Rich A. Competitive behaviour of multiple, discrete B-Z transitions in supercoiled DNA. Proc. Natl. Acad. Sci. USA. 83:1986;6342-6346.
18. Kornberg, A., Baker, D., 1991. DNA Replication. W.H. Freeman, New York.
19. Landy A. Dynamic, structural, and regulatory aspects of λ site-specific recombination. Annu. Rev. Biochem. 58:1989;913-949.
20. Liberman E.A. Cell as a molecular computer (MCC). Biofizika. 17:1972;932-943.
21. Liberman E.A. Analog-digital molecular cell computer. BioSystems. 11:1979;111-124.
22. Lipton R. DNA solution to hard computational problems. Science. 268:1995;542-545.
23. Meisel A., Mackeldanz P., Bickle T.A., Kruger D.H., Schroeder C. Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. EMBO J. 14(12):1995;2958-2966.
24. Nash H.A., Bauer C.E., Gardner J.F. Role of homology in site-specific recombination of bacteriophage: evidence against joining of cohesive ends. Proc. Natl. Acad. Sci. USA. 84:1987;4049-4053.
25. Rothemund, P.W.K., 1996. A DNA and restriction enzyme implementation of turing machines. In: Baum, E.B., Lipton, R.J. (Eds.), DNA Based Computers, vol. 27 of DIMACS: Series in Discrete Mathematics and Theoretical Computer Science. ISSN 1052-1798. American Mathematical Society, 1996, ISBN 08218-0518-5.
26. Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N.V., Goodman, M.F., Rothemund, P.W.K., Adleman, L.M., 1996. A sticker based architecture for DNA computation. AMS, Proceedings of the 2nd Annual Meeting on DNA Based Computers, Princeton University, 10-12 June, 1996, DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, ISSN 1052-1798.
27. Stark W.M., Sherratt D.J., Boocock M.R. Site-specific recombination by Tn3 resolves: topological changes in the forward and reverse reactions. Cell. 58:1989;779-790.
28. Stark W.M., Boocock M.R., Sherratt D.J. Site-specific recombination by Tn3 resolves. Trends Genet. 5(9):1989;304-309.
29. Stark, W.M., Boocock, M.R., 1995. Topological selectivity in site-specific recombination. In: Sherratt, D.J. (Ed.), Mobile Genetic Elements (Frontiers in Molecular Biology Series). Oxford University Press, London, pp. 101-129.
30. Wang J.C. DNA topoisomers. Annu. Rev. Biochem. 54:1985;665-697.
31. Wang, J.C., 1995. Enzymes that supercoil DNA. In: Lilley, D.M. (Ed.), DNA-Protein: Structural Interactions (Frontiers in Molecular Biology Series). Oxford University Press, London, pp. 76-89.
32. Weisberg R.A., Enquist L.W., Foeller C., Landy A. Role for DNA homology in site-specific recombination. J. Mol. Biol. 170:1983;319-342.
33. Yuan R., Hamilton D.L., Burckhardt J. DNA translocation by the restriction enzyme from E. coli K. Cell. 20:1980;237-244.