NMR solution structure of dsDNA containing a bicyclic D-arabino-configured nucleotide fixed in an O4′-endo sugar conformation

Organic and Biomolecular Chemistry

Volumn 1, Issue 10, 2003, Pages 1790-1797

  Tømmerholt, Henning V ^a   Christensen, Nanna K ^a   Nielsen, Poul ^a   Wengel, Jesper ^a   Stein, Paul C ^a   Jacobsen, Jens Peter ^a   Petersen, Michael ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONS; DNA SEQUENCES; ENZYME KINETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STRUCTURE (COMPOSITION); SUGAR (SUCROSE); X RAY CRYSTALLOGRAPHY;

ANTISENSE OLIGONUCLEOTIDES; BICYCLIC ARABINO CONFIGURED NUCLEOTIDE; WATSON-CRICK BASE PAIRING;

DNA;

ARABINOSE; DNA; DRUG DERIVATIVE; OLIGONUCLEOTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; SOLUTION AND SOLUBILITY;

ARABINOSE; BASE SEQUENCE; CARBOHYDRATE CONFORMATION; DNA; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; SOLUTIONS;

EID: 0141940224     PISSN: 14770520     EISSN: None     Source Type: Journal    
DOI: 10.1039/b300848g     Document Type: Article

References (48)

1. W. Saenger, Principles of Nucleic Acid Structure, Springer Verlag, New York, 1984.
2. K. A. Brameld and W. A. Goddard III, J. Am. Chem. Soc., 1999, 121, 985.
3. C. Gonzáles, W. Stec, M. Reynolds and T. L. James, Biochemistry, 1995, 34, 4969.
4. T. E. Cheatham III and P. A. Kollman, J. Am. Chem. Soc., 1997, 119, 4805.
5. J. I. Gyi, A. N. Lane, G. L. Conn and T. Brown, Biochemistry, 1998, 37, 73.
6. S. M. Gryaznov, Biochim. Biophys. Acta, 1999, 1489, 131.
7. I. Berger, V. Tereshko, H. Ikeda, V. E. Marquez and M. Egli, Nucleic Acids Res., 1998, 26, 2473.
8. J.-F. Trempe, C. J. Wilds, A. Y. Denisov, R. T. Pon, M. J. Damha and K. Gehring, J. Am. Chem. Soc., 2001, 123, 4896.
9. A. Y. Denisov, A. M. Noronha, C. J. Wilds, J.-F. Trempe, R. T. Pon, K. Gehring and M. J. Damha, Nucleic Acids Res., 2001, 29, 4284.
10. J.-J. Toulmé and D. Tidd, Role of Ribonuclease H in Antisense Oligonucleotide-Mediated Effects, in Ribonucleases H, ed. R. J. Crouch and J.-J. Toulmé, INSERM, Paris, 1998, 225.
11. O. Y. Fedoroff, M. Salazar and B. R. Reid, J. Mol. Biol., 1993, 233, 509.
12. J. Wengel, Acc. Chem. Res., 1999, 32, 301.
13. P. Herdewijn, Biochim. Biophys. Acta, 1999, 1489, 167.
14. C. J. Leumann, Bioorg. Med. Chem., 2002, 10, 841.
15. M. Meldgaard and J. Wengel, J. Chem. Soc., Perkin Trans 1, 2000, 3539.
16. D. A. Braasch and D. R. Corey, Chem. Biol., 2001, 8, 1.
17. N. K. Christensen, M. Petersen, P. Nielsen, J. P. Jacobsen, C. E. Olsen and J. Wengel, J. Am. Chem. Soc., 1998, 120, 5458.
18. G. A. Jensen, S. K. Singh, R. Kumar, J. Wenger and J. P. Jacobsen, J. Chem. Soc., Perkin Trans. 2, 2001, 1224.
19. D. R. Hare, D. E. Wemmer, S.-H. Chou, G. Drobny and B. R. Reid, J. Mol. Biol., 1983, 171, 319.
20. J. Feigon, W. Leupin, W. A. Denny and D. R. Kearns, Biochemistry, 1983, 22, 5943.
21. R. M. Scheck, N. Russo, R. Boelens and R. Kaptein, J. Am. Chem. Soc., 1983, 105, 2914.
22. K. Wüthrich, NMR of Proteins and Nucleic Acids, John Wiley & Sons, New York, 1986.
23. L. A. Donders, F. A. A. M. de Leeuw and C. Altona, Magn. Reson. Chem., 1989, 27, 556.
24. C. Altona, J. H. Ippel, A. J. A. Westra Hoekzema, C. Erkelens, M. Groesbeek and L. A. Donders, Magn. Reson. Chem., 1989, 27, 564.
25. C. Altona, R. Francke, R. de Haan, J. H. Ippel, G. J. Daalmans, A. J. A. Westra Hoekzema and J. van Wijk, Magn. Reson. Chem., 1994, 32, 670.
26. R. Lavery and H. Sklenar, J. Biomol. Struct. Dyn., 1988, 6, 63.
27. R. Lavery and H. Sklenar, J. Biomol. Struct. Dyn., 1989, 7, 655.
28. N. A. Ulyanov and T. L. James, Methods Enzymol., 1995, 261, 90.
29. C. H. Gotfredsen, H. P. Spielmann, J. Wengel and J. P. Jacobsen, Bioconjugate Chem., 1996, 7, 680.
30. W. D. Cornell, P. Cieplak, I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman, J. Am. Chem. Soc., 1995, 117, 5179.
31. G. Minasov, M. Teplova, P. Nielsen, J. Wengel and M. Egli, Biochemistry, 2000, 39, 3525.
32. The melting temperature of the [3.2.0]bcANA modified duplex was measured under conditions as described by Christensen et al. (ref. 17).
33. M. Petersen, K. Bondensgaard, J. Wengel and J. P. Jacobsen, J. Am. Chem. Soc., 2002, 124, 5974.
34. C. B. Nielsen, S. K. Singh, J. Wengel and J. P. Jacobsen, J. Biomol. Struct. Dyn., 1999, 17, 175.
35. M. Egli, G. Minasov, M. Teplova, R. Kumar and J. Wengel, Chem. Commun., 2001, 651.
36. M. Egli, N. Usman and A. Rich, Biochemistry, 1993, 32, 3221.
37. M. J. Damha, C. J. Wilds, A. Noronha, I. Brukner, G. Borkow, D. Arion and M. A. Parniak, J. Am. Chem. Soc., 1998, 120, 12976.
38. H. Brummel, N. K. Christensen and M. H. Caruthers, Personal communication.
39. L. B. Jørgensen, P. Nielsen, J. Wengel and J.P. Jacobsen, J. Biomol. Struct. Dyn., 2000, 18, 45.
40. S. G. Sarafianos, K. Das, C. Tantillo, A. D. Jr. Clark, J. Ding, J. M. Whitcomb, P. L. Boyer, S. H. Hughes and E. Arnold, EMBO J., 2001, 20, 1449.
41. H. Geen and R. Freeman, J. Magn. Reson., 1991, 93, 93.
42. R. F. Macaya, P. Schultze and J. Feigon, J. Am. Chem. Soc., 1992, 114, 781.
43. C. A. G. Haasnoot, F. A. A. M. de Leeuw and C. Altona, Pseurot 6.2, A Program for the Conformational Analysis of Five Membered Rings; University of Leiden, Leiden, The Netherlands, 1995.
44. K. Bondensgaard, M. Petersen, S.K. Singh, V. K. Rajwanshi, J. Wengel and J.P. Jacobsen, Chem. Eur. J., 2000, 6, 2687.
45. H. Liu, H. P. Spielmann, N. A. Ulyanov, D. E. Wemmer and T. L. James, J. Biomol. NMR, 1995, 6, 390.
46. B. A. Borgias and T. L. James, J. Magn. Reson., 1990, 87, 475.
47. D. A. Case, D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III, W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz, R. V. Stanton, A. L. Cheng, J. J. Vincent, M. Crowley, D. M. Ferguson, R. J. Radmer, G. L. Seibel, U. C. Singh, P. K. Weiner and P. A. Kollman, AMBER 5, University of California, San Francisco, 1997.
48. C. I. Bayly, P. Cieplak, W. D. Cornell and P. A. Kollman, J. Phys. Chem., 1993, 97, 10269.