Chapter 6 Molecular Computing with Deoxyribozymes

Progress in Nucleic Acid Research and Molecular Biology

Volumn 82, Issue , 2008, Pages 199-217

  Stojanovic, Milan N ^a  

^a Och Spine at New York Presbyterian Hospitals

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBOZYME;

AUTOMATION; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; LOGIC; MATHEMATICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REVIEW;

AUTOMATION; BASE SEQUENCE; CATALYSIS; DNA, CATALYTIC; LOGIC; MATHEMATICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION;

EID: 53049086688     PISSN: 00796603     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6603(08)00006-8     Document Type: Review

References (31)

1. Adleman L.M. Molecular computation of solutions to combinatorial problems. Science 266 5187 (1994) 1021-1024
2. de Silva A.P., Leydet Y., Lincheneau C., and McClenaghan N.D. Chemical approaches to nanometre-scale logic gates. J. Phys. Condens. Matter 18 33 (2006) S1847-S1872
3. Credi A. Molecules that make decisions 46 29 (2007) 5472-5475
4. Breaker R.R. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13 (2002) 31-39
5. Breaker R.R., and Joyce G.F. A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity. Chem. Biol. 2 10 (1995) 655-660
6. Santoro S.W., and Joyce G.F. Proc. Natl. Acad. Sci. USA 94 (1997) 4262-4266
7. Tyagi S., and Krammer F.R. Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol. 14 (1996) 303-309
8. Stojanovic M.N., de Prada P., and Landry D.W. Catalytic molecular beacons. ChemBioChem 2 6 (2001) 411-415
9. Stojanovic M.N., Mitchell T.E., and Stefanovic D. Deoxyribozyme-based logic gates. J. Am. Chem. Soc. 124 14 (2002) 3555-3561
10. Stojanovic M.N., and Stefanovic D. A deoxyribozyme-based molecular automaton. Nat. Biotechnol. 21 9 (2003) 1069-1074
11. Yurke B., Turberfield A.J., Mills Jr. A.P., Simmel F.C., and Neumann J.L. A DNA-fuelled molecular machine made of DNA. Nature 406 6796 (2000) 605-608
12. Lederman H., Macdonald J., Stefanovic D., and Stojanovic M.N. Deoxyribozyme-based three-input logic gates and construction of a molecular full adder. Biochemistry 45 4 (2006) 1194-1199
13. Macdonald J., Stefanovic D., and Stojanovic M.N. Solution-phase molecular-scale computation with deoxyribozyme-based logic gates and fluorescent readouts. In: Didenko V. (Ed). Fluorescent Energy Transfer Nucleic Acid Probes: Designs and Protocols 335 (2006), Humana Press, Totowa, NJ 343-363
14. McCluskey E.J. Logic Design Principles: With Emphasis on Testable Semicustom Circuits. (1986), Prentice Hall, Englewood Cliffs, NJ
15. Stojanovic M.N., and Stefanovic D. Deoxyribozyme-based half adder. J. Am. Chem. Soc. 125 (2003) 6673-6676
16. Macdonald J., Sutovic M., Lederman H., Pendri K., Lu W., Andrews B.L., Stefanovic D., and Stojanovic M.N. Medium scale integration of molecular logic gates in an automaton. Nano Lett. 6 11 (2006) 2598-2603
17. Penchovsky R., and Breaker R.R. Nat. Biotechnol. 23 (2005) 1424-1433
18. Cuenoud B., and Szostak J.W. Nature 375 (1995) 611-614
19. Stojanovic M.N., Semova S., Kolpashchikov D., Macdonald J., Morgan C., and Stefanovic D. Deoxyribozyme-based ligase logic gates and their initial circuits. J. Am. Chem. Soc. 127 (2005) 6914-6915
20. Stojanovic M.N., de Prada P., and Landry D.W. Nucleic Acids Res. 28 (2000) 2915-2918
21. Kolpashchikov D.M., and Stojanovic M.N. Boolean control of aptamer binding States. J. Am. Chem. Soc. 127 32 (2005) 11348-11351
22. Nutiu R., and Li Y. Structure-switching signaling aptamers. J. Am. Chem. Soc. 125 16 (2003) 4771-4778
23. Dittmer W.U., Reuter A., and Simmel F.C. A DNA-based machine that can cyclically bind and release thrombin. Angew. Chem. Int. Ed. Engl. 43 27 (2004) 3550-3553
24. Dirks R.M., and Pierce N.A. Triggered amplification by hybridization chain reaction. Proc. Natl. Acad. Sci. USA 101 43 (2004) 15275-15278
25. Ruslan Y., Sergei R., and Milan N.S. Networking particles over distance using oligonucleotide-based devices. J. Am. Chem. Soc. 129 50 (2007) 15581-15584
26. Carbone A., and Seeman N.C. Circuits and programmable self-assembling DNA structures. Proc. Natl. Acad. Sci. 99 (2002) 12577-12582
27. Rothemund P.W.K., Papadakis N., and Winfree E. Algorithmic self-assembly on DNA sierpinski triangles. PLoS Biol. 2 (2004) e424
28. Georg S., David S., and David Y.Z. Erik winfree enzyme-free nucleic acid logic circuits. Science 314 5805 (2006) 1585-1588
29. Rothemund P.W.K. A DNA and restriction enzyme implementation of Turing machines. In DNA Based Computers, Proceedings of a DIMACS Workshop, April 1995 (1995) 75-119
30. Benenson Y., Paz-Elizur T., Adar R., Keinan E., Livneh Z., and Shapiro E. Programmable and autonomous computing machine made of biomolecules. Nature 414 (2001) 430-434
31. Benenson Y., Gil B., Ben-Dor U., Adar R., and Shapiro E. An autonomous molecular computer for logical control of gene expression. Nature 429 (2004) 423-429