Topological links between duplex DNA and a circular DNA single strand

Angewandte Chemie - International Edition

Volumn 38, Issue 10, 1999, Pages 1446-1449

  Kuhn, Heiko ^a   Demidov, Vadim V ^a   Frank Kamenetskii, Maxim D ^a  

^a Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; SINGLE STRANDED DNA;

ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; DNA PROBE; DNA STRUCTURE; ISOMERISM; SEQUENCE ANALYSIS;

EID: 0033577866     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-3773(19990517)38:10<1446::AID-ANIE1446>3.0.CO;2-3     Document Type: Article

References (28)

1. a) M. D. Frank-Kamenetskii, J. Mol. Struct. (Theochem) 1995, 336, 235-243;
2. b) N. C. Seeman, Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 225-248;
3. c) K. Ryan, E. T. Kool, Chem. Biol. 1998, 5, 59-67;
4. d) N. C. Seeman, Angew. Chem. 1998, 110, 3408-3428;
5. Angew. Chem. Int. Ed. 1998, 37, 3220-3238.
6. a) M. D. Frank-Kamenetskii, Unraveling DNA: The most important molecule of life, Addison-Wesley, Reading, MA, USA, 1997, p. 214;
7. b) R. Sinden, DNA Structure and Function, Academic Press, San Diego, CA, USA, 1994, p. 398.
8. a) N. C. Seeman, Acc. Chem. Res. 1997, 30, 357-363;
9. b) C. M. Niemeyer, Angew. Chem. 1997, 109, 603-606;
10. Angew. Chem. Int. Ed. Engl. 1997, 36, 585-587.
11. a) M. Nilsson, H. Malmgren, M. Samiotaki, M. Kwiatkowski, B. P. Chowdhary, U. Landegren, Science 1994, 265, 2085-2088;
12. b) M. Nilsson, K. Krejci, J. Koch, M. Kwiatkowski, P. Gustavsson, U. Landegren, Nat. Gen. 1997, 16, 252-254;
13. c) P. M. Lizardi, X. Huang, Z. Zhu, P. Bray-Ward, D. C. Thomas, D. C. Ward, Nat. Gen. 1998, 19, 225-232;
14. d) J. Banér, M. Nilsson, M. Mendel-Hartvig, U. Landegren, Nucleic Acids Res. 1998, 26, 5073-5078.
15. a) N. O. Bukanov, V. V. Demidov, P. E. Nielsen, M. D. Frank-Kamenetskii, Proc. Natl. Acad. Sci. USA 1998, 95, 5516-5520;
16. b) V. V. Demidov, N. O. Bukanov, M. D. Frank-Kamenetskii in PNA: Protocols and Applications (Eds.: P. E. Nielsen, M. Egholm), Horizon Scientific, Wymondham, UK, 1999, pp. 187-195.
17. a) P. E. Nielsen, Pure Appl. Chem. 1998, 70, 105-110;
18. b) E. Uhlmann, A. Peyman, G. Breipohl, D. W. Will, Angew. Chem. 1998, 110, 2954-2983;
19. Angew. Chem. Int. Ed. 1998, 37, 2796-2823.
20. The optimal yield of linked product III is about 70-80% after a single ligation step. The major factor affecting the yield is the ODN concentration: the yield of III decreases significantly when the ODN concentration is too low (<0.1 μM) or too high (> 1 μM). Still, under optimal conditions 20 to 30% of the dsDNA molecules remain topologically unlinked with cODN. A second round of ligation, which is performed after dissociation at elevated temperatures of ODNs bound to and yet unlinked with dsDNA, results in virtually quantitative yield of linked products.
21. a) V. V. Demidov, M. V. Yavnilovich, M. D. Frank-Kamenetskii, Biophys. J. 1997, 72, 2763-2769;
22. b) H. Kuhn, V. V. Demidov, M. D. Frank-Kamenetskii, P. E. Nielsen, Nucleic Acids Res. 1998, 26, 582-587.
23. a) U. Landegren, R. Kaiser, J. Sanders, L. Hood, Science 1988, 241, 1077-1080;
24. b) D. Y. Wu, R. B. Wallace, Gene 1989, 76, 245-254;
25. c) K. Harada, L. E. Orgel, Nucleic Acids Res. 1993, 21, 2287-2291.
26. [4a]
27. a) M. Egholm, L. Christensen, K. L. Dueholm, O. Buchardt, J. Coull, P. E. Nielsen, Nucleic Acids Res. 1995, 23, 217-222;
28. b) L. Christensen., R. Fitzpatrick, B. Gildea, K. H. Petersen, H. F. Hansen, T. Koch, M. Egholm, O. Buchardt, P. E. Nielsen, J. Coull, R. H. Berg, J. Peptide Sci. 1995, 3, 175-183.