Identification and characterization of second-generation invader locked nucleic acids (LNAs) for mixed-sequence recognition of double-stranded DNA

Journal of Organic Chemistry

Volumn 78, Issue 19, 2013, Pages 9560-9570

  Sau, Sujay P ^a   Madsen, Andreas S ^b   Podbevsek, Peter ^c   Andersen, Nicolai K ^b   Kumar, T Santhosh ^b   Andersen, Sanne ^a,b   Rathje, Rie L ^a,b   Anderson, Brooke A ^a   Guenther, Dale C ^a   Karmakar, Saswata ^a   Kumar, Pawan ^a   Plavec, Janez ^c   Wengel, Jesper ^b   Hrdlicka, Patrick J ^a  

^a UNIVERSITY OF IDAHO   (United States)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DOUBLE-STRANDED DNA (DS-DNA); LOCKED NUCLEIC ACID; PEPTIDE NUCLEIC ACID; SECOND GENERATION; STRUCTURAL FACTOR; THERMAL DENATURATIONS; TRIPLEX-FORMING OLIGONUCLEOTIDES;

BIOMOLECULES; FLUORESCENCE SPECTROSCOPY; LOCKS (FASTENERS); MONOMERS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OLIGONUCLEOTIDES; PROBES; RNA; SCAFFOLDS;

DNA;

COMPLEMENTARY DNA; DOUBLE STRANDED DNA; LOCKED NUCLEIC ACID; MOLECULAR SCAFFOLD; MONOMER; PYRENE;

ARTICLE; CONTROLLED STUDY; DNA DENATURATION; DNA HAIRPIN; DNA PROBE; FLUORESCENCE SPECTROSCOPY; MOLECULAR MODEL; MOLECULAR RECOGNITION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STEADY STATE; STRUCTURE ANALYSIS; THERMAL ANALYSIS; THERMOSTABILITY;

DNA; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; PYRENES; SPECTROMETRY, FLUORESCENCE; THYMIDINE MONOPHOSPHATE;

EID: 84885099980     PISSN: 00223263     EISSN: 15206904     Source Type: Journal    
DOI: 10.1021/jo4015936     Document Type: Article

References (63)

1. Rogers, F. A.; Lloyd, J. A.; Glazer, P. M. Curr. Med. Chem.: Anti-Cancer Agents 2005, 5, 319-326
2. Ghosh, I.; Stains, C. I.; Ooi, A. T.; Segal, D. J. Mol. BioSyst. 2006, 2, 551-560
3. Nielsen, P. E. ChemBioChem 2010, 11, 2073-2076
4. Mukherjee, A.; Vasquez, K. M. Biochimie 2011, 93, 1197-1208
5. Aiba, Y.; Sumaoka, J.; Komiyama, M. Chem. Soc. Rev. 2011, 40, 5657-5668
6. Vaijayanthi, T.; Bando, T.; Pandian, G. N.; Sugiyama, H. ChemBioChem 2012, 13, 2170-2185
7. Simon, P.; Cannata, F.; Concordet, J.-P.; Giovannangeli, C. Biochimie 2008, 90, 1109-1116
8. Duca, M.; Vekhoff, P.; Oussedik, K.; Halby, L.; Arimondo, P. B. Nucleic Acids Res. 2008, 36, 5123-5138
9. Kaihatsu, K.; Janowski, B. A.; Corey, D. R. Chem. Biol. 2004, 11, 749-758
10. Nielsen, P. E. Chem. Biodiversity 2010, 7, 786-804
11. Dervan, P. B.; Edelson, B. S. Curr. Opin. Struct. Biol. 2003, 13, 284-299
12. Kutyavin, I. V.; Rhinehart, R. L.; Lukhtanov, E. A.; Gorn, V. V.; Meyer, R. B., Jr.; Gamper, H. B., Jr. Biochemistry 1996, 35, 11170-11176
13. Lohse, J.; Dahl, O.; Nielsen, P. E. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11804-11808
14. Ishizuka, T.; Yoshida, J.; Yamamoto, Y.; Sumaoka, J.; Tedeschi, T.; Corradini, R.; Sforza, S.; Komiyama, M. Nucleic Acids Res. 2008, 36, 1464-1471
15. Janowski, B. A.; Kaihatsu, K.; Huffman, K. E.; Schwartz, J. C.; Ram, R.; Hardy, D.; Mendelson, C. R.; Corey, D. R. Nat. Chem. Biol. 2005, 1, 210-215
16. Beane, R.; Gabillet, S.; Montaillier, C.; Arar, K.; Corey, D. R. Biochemistry 2008, 47, 13147-13149
17. Rapireddy, S.; Bahal, R.; Ly, D. H. Biochemistry 2011, 50, 3913-3918
18. Bahal, R.; Sahu, B.; Rapireddy, S.; Lee, C.-M.; Ly, D. H. ChemBioChem 2012, 13, 56-60
19. Rusling, D. A.; Powers, V. E. C.; Ranasinghe, R. T.; Wang, Y.; Osborne, S. D.; Brown, T.; Fox, K. Nucleic Acids Res. 2005, 33, 3025-3032
20. Hari, Y.; Obika, S.; Imanishi, T. Eur. J. Org. Chem. 2012, 2875-2887
21. Bogdanove, A. J.; Voytas, D. F. Science 2011, 333, 1843-1846
22. Gaj, T.; Gersbach, C. A.; Barbas, C. F., III. Trends Biotechnol. 2013, 31, 397-405
23. Tse, W. C.; Boger, D. L. Chem. Biol 2004, 11, 1607-1617
24. Hamilton, P. L.; Arya, D. P. Nat. Prod. Rep. 2012, 29, 134-143
25. Bryld, T.; Højland, T. R.; Wengel, J. Chem. Commun. 2004, 1064-1065
26. Filichev, V. V.; Vester, B.; Hansen, L. H.; Pedersen, E. B. Nucleic Acids Res. 2005, 33, 7129-7137
27. Ge, R.; Heinonen, J. E.; Svahn, M. G.; Mohamed, A. J.; Lundin, K. E.; Smith, C. I. E. FASEB J. 2007, 21, 1902-1914
28. Moreno, P. M. D.; Geny, S.; Pabon, Y. V.; Bergquist, H.; Zaghloul, E. M.; Rocha, C. S. J.; Oprea, I. I.; Bestas, B.; Andaloussi, S. E. L.; Jørgensen, P. T.; Pedersen, E. B.; Lundin, K. E.; Zain, R.; Wengel, J.; Smith, C. I. E. Nucleic Acids Res. 2013, 41, 3257-3273
29. Hrdlicka, P. J.; Kumar, T. S.; Wengel, J. Chem. Commun. 2005, 4279-4281
30. Sau, S. P.; Kumar, T. S.; Hrdlicka, P. J. Org. Biomol. Chem. 2010, 8, 2028-2036
31. Kumar, T. S.; Madsen, A. S.; Østergaard, M. E.; Sau, S. P.; Wengel, J.; Hrdlicka, P. J. Org. Chem. 2009, 74, 1070-1081
32. Nielsen, C. B.; Petersen, M.; Pedersen, E. B.; Hansen, P. E.; Christensen, U. B. Bioconjugate Chem. 2004, 15, 260-269
33. Karmakar, S.; Anderson, B. A.; Rathje, R. L.; Andersen, S.; Jensen, T.; Nielsen, P.; Hrdlicka, P. J. J. Org. Chem. 2011, 76, 7119-7131
34. Kalra, N.; Babu, B. R.; Parmar, V. S.; Wengel, J. Org. Biomol. Chem. 2004, 2, 2885-2887
35. Nakamura, M.; Fukunaga, Y.; Sasa, K.; Ohtoshi, Y.; Kanaori, K.; Hayashi, H.; Nakano, H.; Yamana, K. Nucleic Acids Res. 2005, 33, 5887-5895
36. Didion, B. A.; Karmakar, S.; Guenther, D. C.; Sau, S. P.; Verstegen, J. P.; Hrdlicka, P. J. ChemBioChem 2013, 4, 3447-3454
37. Denn, B.; Karmakar, S.; Guenther, D. C.; Hrdlicka, P. J. Chem. Commun. 10.1039/C3CC45705B
38. Kumar, T. S.; Madsen, A. S.; Wengel, J.; Hrdlicka, P. J. J. Org. Chem. 2006, 71, 4188-4201
39. Andersen, N. K.; Wengel, J.; Hrdlicka, P. J. Nucleosides, Nucleotides Nucleic Acids 2007, 26, 1415-1417
40. The synthesis of monomer M will be published elsewhere.
41. Winnik, F. M. Chem. Rev. 1993, 93, 587-614
42. Dioubankova, N. N.; Malakhov, A. D.; Stetsenko, D. A.; Gait, M. J.; Volynsky, P. E.; Efremov, R. G.; Korshun, V. A. ChemBioChem 2003, 4, 841-847
43. Astakhova, I. V.; Malakhov, A. D.; Stepanova, I. A.; Ustinov, A. V.; Bondarev, S. L.; Paramonov, A. S.; Korshun, V. A. Bioconjugate Chem. 2007, 18, 1972-1980
44. Astakhova, I. V.; Ustinov, A. V.; Korshun, V. A.; Wengel, J. Bioconjugate Chem. 2011, 22, 533-539
45. Hrdlicka, P. J.; Babu, B. R.; Sørensen, M. D.; Wengel, J. Chem. Commun. 2004, 1478-1479
46. Hwang, G. T.; Seo, Y. J.; Kim, B. H. Tetrahedron Lett. 2005, 46, 1475-1477
47. Grünewald, C.; Kwon, T.; Piton, N.; Förster, U.; Wachtveitl, J.; Engels, J. W. Bioorg. Med. Chem. 2008, 16, 19-26
48. Nakamura, M.; Murakami, Y.; Sasa, K.; Hayashi, H.; Yamana, K. J. Am. Chem. Soc. 2008, 130, 6904-6905
49. Astakhova, I. V.; Lindegaard, D.; Korshun, V. A.; Wengel, J. Chem. Commun. 2010, 46, 8362-8364
50. Seela, F.; Ingale, S. A. J. Org. Chem. 2010, 75, 284-295
51. Ingale, S. A.; Pujari, S. S.; Sirivolu, V. R.; Ding, P.; Xiong, H.; Mei, H.; Seela, F. J. Org. Chem. 2012, 77, 188-199
52. Kumar, P. K.; Shaikh, K. I.; Jørgensen, A. S.; Kumar, S.; Nielsen, P. J. Org. Chem. 2012, 77, 9562-9573
53. Langenegger, S. M.; Häner, R. Chem. Commun. 2004, 2792-2793
54. Haner, R.; Garo, F.; Wenger, D.; Malinovskii, V. L. J. Am. Chem. Soc. 2010, 132, 7466-7471
55. Wojciechowski, F.; Lietard, J.; Leumann, C. J. Org. Lett. 2012, 14, 5176-5179
56. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197
57. Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829
58. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129
59. MacroModel, version 9.8; Schrödinger, LLC: New York, 2010.
60. Crothers, D. M. Biopolymers 1968, 6, 575-584
61. Wadkins, R. M. Curr. Med. Chem. 2000, 7, 1-15
62. Keene, F. R.; Smith, J. A.; Collins, J. G. Coord. Chem. Rev. 2009, 253, 2021-2035
63. Nakamura, M.; Shimomura, Y.; Ohtoshi, Y.; Sasa, K.; Hayashi, H.; Nakano, H.; Yamana, K. Org. Biomol. Chem. 2007, 5, 1945-1951