Deoxyribozyme-based three-input logic gates and construction of a molecular full adder

Biochemistry

Volumn 45, Issue 4, 2006, Pages 1194-1199

  Lederman, Harvey ^a   Macdonald, Joanne ^a   Stefanovic, Darko ^b   Stojanovic, Milan N ^a  

^a Columbia University ^*  (United States)

^b University of NewMexico   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADDERS; ARRAYS; AUTONOMOUS AGENTS; DIAGNOSTIC RADIOGRAPHY; ENZYMES; HYDRATION; MOLECULAR BIOLOGY;

ANDAND GATE; ANDNOTANDNOT GATES; FLUOROGENIC CLEAVAGE REACTIONS; OLIGONUCLEOTIDES;

ENZYME KINETICS;

DEOXYRIBOZYME; OLIGONUCLEOTIDE;

AQUEOUS HUMOR; ARITHMETIC; ARTICLE; AUTOMATION; CALCULATION; CHEMICAL ENGINEERING; DEVICE; LOGIC; MATHEMATICAL ANALYSIS; MOLECULAR FULL ADDER; MOLECULAR HYBRIDIZATION; MOLECULAR INTERACTION; MOLECULAR LOGIC GATE; PRIORITY JOURNAL;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA, CATALYTIC; LOGIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; SOLUTIONS; TIME FACTORS;

EID: 31544432270     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi051871u     Document Type: Article

References (23)

1. Benner, S. A., and Sismour, A. M. (2005) Synthetic biology, Nat. Rev. Genet. 6, 533-543.
2. Margolin, A. A., and Stojanovic, M. N. (2005) Boolean calculations made easy (for ribozymes), Nat. Biotechnol. 23, 1374-1376.
3. Stojanovic, M. N., de Prada, P., and Landry, D. W. (2001) Catalytic molecular beacons, ChemBioChem. 2, 411-415.
4. Burke, D. H., Ozerova, N. D., and Nilsen-Hamilton, M. (2002) Allosteric hammerhead ribozyme TRAPs, Biochemistry 41, 6588-6594.
5. Porta, H., and Lizardi, P. M. (1995) An allosteric hammerhead ribozyme, Biotechnology (New York) 13, 161-164.
6. Komatsu, Y., Yamashita, S., Kazama, N., Nobuoka, K., and Ohtsuka, E. (2000) Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor, J. Mol. Biol. 299, 1231-1243.
7. Wang, D. Y., and Sen, D. (2001) A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate, J. Mol. Biol. 310, 723-734.
8. Robertson, M. P., and Ellington, A. D. (2000) Design and optimization of effector-activated ribozyme ligases, Nucleic Acids Res. 28, 1751-1759.
9. Lorsch, J. R., and Szostak, J. W. (1995) Kinetic and thermodynamic characterization of the reaction catalyzed by a polynucleotide kinase ribozyme, Biochemistry 34, 15315-15327.
10. Tanabe, T., Kuwabara, T., Warashina, M., Tani, K., Taira, K., and Asano, S. (2000) Oncogene inactivation in a mouse model, Nature 406, 473-474.
11. Stojanovic, M. N., Mitchell, T. E., and Stefanovic, D. (2002) Deoxyribozyme-based logic gates, J. Am. Chem. Soc. 124, 3555-3561.
12. Stojanovic, M. N., and Stefanovic, D. (2003) Deoxyribozyme-based half-adder, J. Am. Chem. Soc. 125, 6673-6676.
13. Stojanovic, M. N., and Stefanovic, D. (2003) A deoxyribozyme-based molecular automaton, Nat. Biotechnol. 21, 1069-1074.
14. Stojanovic, M. N., Semova, S., Kolpashchikov, D., Macdonald, J., Morgan, C., and Stefanovic, D. (2005) Deoxyribozyme-based ligase logic gates and their initial circuits, J. Am. Chem. Soc. 127, 6914-6915.
15. Kolpashchikov, D. M., and Stojanovic, M. N. (2005) Boolean control of aptamer binding states, J. Am. Chem. Soc. 127, 11348-11351.
16. de Silva, A. P., and McClenaghan, N. D. (2004) Molecular-scale logic gates, Chemistry 10, 574-586.
17. de Silva, A. P., and McClenaghan, N. D. (2000) Proof-of-principle of molecular-scale arithmetic, J. Am. Chem. Soc. 122, 3965-3966.
18. Remade, F., Speiser, S., and Levine, R. D. (2001) Intermolecular and intramolecular logic gates, J. Phys. Chem. B 105, 5589-5591.
19. Okamoto, A., Tanaka, K., and Saito, I. (2004) DNA logic gates, J. Am. Chem. Soc. 126, 9458-9463.
20. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res. 31, 3406-3415.
21. Breaker, R. R., and Joyce, G. F. (1995) A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity, Chem. Biol. 2, 655-660.
22. Santoro, S. W., and Joyce, G. F. (1997) A general purpose RNA-cleaving DNA enzyme, Proc. Natl. Acad. Sci. U.S.A. 94, 4262-4266.
23. Yurke, B., Turberfield, A. J., Mills, A. P., Jr., Simmel, F. C., and Neumann, J. L. (2000) A DNA-fuelled molecular machine made of DNA, Nature 406, 605-608.