DNA word design strategy for creating sets of non-interacting oligonucleotides for DNA microarrays

Langmuir

Volumn 18, Issue 3, 2002, Pages 805-812

  Li, Ming ^a   Lee, Hye Jin ^a   Condon, Anne E ^b   Corn, Robert M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSENSORS; NANOSTRUCTURED MATERIALS; SYNTHESIS (CHEMICAL); THERMODYNAMICS;

OLIGONUCLEOTIDES;

DNA;

EID: 0037022484     PISSN: 07437463     EISSN: None     Source Type: Journal    
DOI: 10.1021/la0112209     Document Type: Article

References (32)

1. Lin, V.S.-Y.; Motesharei, K.; Dancil, K.-P.S.; Sailor, M.J.; Ghadiri, M.R. Science 1997, 278, 840-843.
2. Chee, M.; Yang, R.; Hubbell, E.; Berno, A.; Huang, X.C.; Stern, D.; Winkler, J.; Lockhart, D.J.; Morris, M.S.; Fodor, S.P.A. Science 1996, 274, 610-614.
3. Southern, E.M.; Case-Green, S.C.; Elder, J.K.; Johnson, M.; Mir, K.U.; Wang, L.; Williams, J.C. Nucleic Acids. Res. 1994, 22, 1368-1373.
4. Frutos, A.G.; Liu, Q.; ThieI, A.J.; Sanner, A.W.; Condon, A.E.; Smith, L.M.; Corn, R.M. Nucleic Acids Res. 1997, 25, 4748-4757.
5. Frutos, A.G.; Smith, L.M.; Corn, R.M. J. Am. Chem. Soc. 1998, 120, 10277-10282.
6. Liu, Q.; Wang, L.; Frutos, A.G.; Condon, A.E.; Corn, R.M.; Smith, L.M. Nature 2000, 403, 175-179.
7. Liu, J.; Zhang, Q.; Remsen, E.E.; Wooley, K.L. Biomacromolecules 2001, 2, 362-368.
8. Brenner, S.; Johnson, M.; Bridgham, J.; Golda, G.; Lloyd, D.H.; Johnson, D.; Luo, S.; McCurdy, S.; Foy, M.; Ewan, M.; Roth, R.; George, D.; Eletr, S.; Albrecht, G.; Vermaas, E.; Williams, S.R.; Moon, K.; Burcham, T.; Pallas, M.; DuBridge, R.B.; Kirchner, J.; Fearon, K.; Mae, J.; Corcoran, K. Nat. Biotechnol. 2009, 18 (6), 630-634.
9. Winzeler, E.A.; Richards, D.R.; Conway, A.R.; Goldstein, A.L.; Kahnan, S.; McCullough, M.J.; McCusker, J.H.; Stevens, D.A.; Wodicka, L.; Lockhart, D.J.; Davis, R.W. Science 1998, 281, 1194-1197.
10. Schena, M.; Shalon, D.; Davis, R.W.; Brown, P.O. Science 1995, 270, 467-470.
11. Pease, A.C.; Solas, D.; Sullivan, E.J.; Cronin, M.T.; Holmes, C.P.; Fodor, S.P.A. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 5022-5026.
12. Braich, R.S.; Johnson, C.; Rothemud, P.W.K.; Hwang, D.; Chelyapov, N.; Adleman, L.M. Solution or a satisfiability problem on a gel based DNA computer; The Netherlands: Leiden, June, 2000.
13. Faulhammer, D.; Cukras, A.R.; Lipton, R.J.; Landweber, L.F. Proc. Natl. Acad. Sci. 2000, 97 (4), 1385-1389.
14. Sakamoto, K.; Gouzu, H.; Komiya, K.; Kiga, D.; Yokoyama, S.; Yokomori, T.; Hagiya, M. Science 2000, 288, 1223-1226.
15. Brenner, S. Methods for Sorting Polynucleotides using Oligonucleotide Tags. U.S.A. patent dated Feb 18, 1997, ISBN # 5604097.
16. Shoemaker, D.D.; Lashkari, D.A.; Morris, D.; Mittman, M.; Davis, R.W. Nat. Genet. 1996, 16, 450-456.
17. Mir, K.U. A Restricted Genetic Alphabet for DNA Computing. Proceedings of DNA Based Computers II, DIMACS Workshop, June 10-12, 1996; Landweber, L.F., Baum, E.B., Eds.; DIMACS Ser. Discrete Math. Theor. Comput. Sci. 1999, 44, 243-246.
18. Mir, K.U. A Restricted Genetic Alphabet for DNA Computing. Proceedings of DNA Based Computers II, DIMACS Workshop, June 10-12, 1996; Landweber, L.F., Baum, E.B., Eds.; DIMACS Ser. Discrete Math. Theor. Comput. Sci. 1999, 44, 243-246.
19. Deaton, R.; Garzon, M.; Murphy, R.C.; Rose, J.A.; Franceschetti, D.R.; Stevens, S.E., Jr. In Genetic Search of Reliable Encodings for DNA-Based Computation; Koza, J.R., Goldberg, D.E., Fogel, D.B., Riolo, R.L., Eds.; Proceedings of the First Annual Conference on Genetic Programming; 1996.
20. Baum, E.B. DNA Sequences Useful for Computation. Proc. 2nd DIMACS Workshop on DNA Bases Computers; June 1996.
21. Deaton, R.; Murphy, R.C.; Garzon, M.; Franceschetti, D.R.; Stevens, S.E., Jr. Good Encoding for DNA-Based Solutions to Combinatorial Problems. Proc. of DNA Based Computers II, DIMACS Workshop, June 10-12, 1996; Landweber, L.F., Baum, E.B., Eds.; DIMACS Ser. Discrete Math. Theor. Comput. Sci. 1999, 44, 247-258.
22. Deaton, R.; Murphy, R.C.; Garzon, M.; Franceschetti, D.R.; Stevens, S.E., Jr. Good Encoding for DNA-Based Solutions to Combinatorial Problems. Proc. of DNA Based Computers II, DIMACS Workshop, June 10-12, 1996; Landweber, L.F., Baum, E.B., Eds.; DIMACS Ser. Discrete Math. Theor. Comput. Sci. 1999, 44, 247-258.
23. Adleman, L.M. Science 1994, 266, 1021-1024.
24. Brenner, S.; Lerner, R.A. Proc. Natl. Acad. Sci. 1992, 89, 5381-5383.
25. Liu, Q.; Frutos, A.G.; Thiel, A.J.; Corn, R.M.; Smith, L.M. J. Comput. Biol. 1998, 5, 269-278.
26. Hanken, D.G.; Corn, R.M. Anal. Chem. 1995, 67, 3767-3774.
27. Nelson, B.P.; Frutos, A.G.; Brockman, J.M.; Corn, R.M. Anal. Chem. 1999, 71, 3935-3940.
28. User Guide to DNA Modification and Labeling; Glen Research Corporation: Sterling, VA, 1990.
29. Jordan, C.E.; Frutos, A.G.; Thiel, A.J.; Corn, R.M. Anal. Chem. 1997, 69, 4939-4947.
30. Brockman, J.M.; Frutos, A.G.; Corn, R.M. J. Am. Chem. Soc. 1999, 121, 8044-8051.
31. MacWilliams, F.J.; Sloane, N.J.A. In The theory of error correcting codes; Artin, H., Bass, H., Eells, J., Feit, W., Freyd, P.J., Gehring, F.W., Halberstam, H., Hormauder, L.V., Kac, M., Kemperman, J.H.B., Lauwerier, H.A., Luxemburg, W.A.J., Peterson, F.P., Singer, I.M., Zaanen, A.C., Eds.; North-Holland Publishing Company: Amsterdam, New York, Oxford, 1978; Vol. 16, pp 1-58 and 673-690.
32. Breslauer, K.J.; Frank, R.; Blöcker, H.; Marky, L.A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3746-3750.