Loop and backbone modifications of peptide nucleic acid improve G-quadruplex binding selectivity

Journal of the American Chemical Society

Volumn 131, Issue 51, 2009, Pages 18415-18424

  Lusvarghi, Sabrina ^a   Murphy, Connor T ^a   Roy, Subhadeep ^a   Tanious, Farial A ^b   Sacui, Iulia ^a   Wilson, W David ^b   Ly, Danith H ^a   Armitage, Bruce A ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b GEORGIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTI-CANCER AGENTS; BINDING SELECTIVITY; CHIRAL MODIFICATION; COMPLEMENTARY SEQUENCES; DUPLEX FORMATION; G-QUADRUPLEXES; GUANINE; HIGH AFFINITY; NEW STRATEGY; PEPTIDE NUCLEIC ACID; QUADRUPLEX STRUCTURES; SURFACE PLASMONS;

BIOACTIVITY; DNA; GENE EXPRESSION; GENE EXPRESSION REGULATION; NUCLEIC ACIDS; OLIGOMERS; PEPTIDES; POSITIVE IONS; RNA; SURFACE PLASMON RESONANCE;

DNA SEQUENCES;

GUANINE QUADRUPLEX; PEPTIDE NUCLEIC ACID;

ARTICLE; BINDING AFFINITY; CHIRALITY; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENE TARGETING; NUCLEIC ACID STRUCTURE; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; PROTEIN DNA BINDING; PROTEIN MODIFICATION; SURFACE PLASMON RESONANCE; ULTRAVIOLET RADIATION;

DRUG DESIGN; G-QUADRUPLEXES; GENE EXPRESSION REGULATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; PEPTIDE NUCLEIC ACIDS; SURFACE PLASMON RESONANCE;

EID: 73249118663     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja907250j     Document Type: Article

References (59)

1. Watson, J. D.; Crick, F. H. C. Nature 1953, 171, 737-738.
2. Gellert, M.; Lipsett, M. N.; Davies, D. R. Proc. Natl. Acad. Sci. U.S.A. 1962, 48, 2013-2018.
3. Arnott, S.; Chandrasekaran, R.; Marttila, C. M. Biochem. J. 1974, 141, 537-543.
4. Blackburn, E. H. Nature 1991, 350, 569-753.
5. Blackburn, E. H. Science 1990, 249, 489-490.
6. Hardin, C. C.; Henderson, E.; Watson, T.; Prosser, J. K. Biochemistry 1991, 30, 4460-4472.
7. Oka, Y.; Thomas, C. A., Jr. Nucleic Acids Res. 1987, 15, 8877-8898.
8. Sundquist, W. I.; Klug, A. Nature (London, U.K.) 1989, 342, 825-829.
9. Huppert, J. L.; Balasubramanian, S. Nucleic Acids Res. 2005, 33, 2908-2916.
10. Todd, A. K.; Johnston, M.; Neidle, S. Nucleic Acids Res. 2005, 33, 2901-2907.
11. Huppert, J.; Balasubramanian, S. Nucleic Acids Res. 2007, 35, 406-413.
12. Zhao, Y.; Du, Z.; Li, N. FEBS Lett. 2007, 581, 1951-1956.
13. Viglasky, V. FEBS J. 2009, 276, 401-409.
14. Patel, D. J.; Phan, A. T.; Kuryavyi, V. Nucleic Acids Res. 2007, 35, 7429-7455.
15. Maizels, N. Nat. Struct. Mol. Biol. 2006, 13, 1055-1059.
16. Siddiqui-Jain, A.; Grand, C. L.; Bearss, D. J.; Hurley, L. H. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11593-11598.
17. Qin, Y.; Hurley, L. H. Biochimie 2008, 90, 1149-1171.
18. Gomez, D.; Lemarteleur, T.; Lacroix, L.; Mailliet, P.; Mergny, J.-L.; Riou, J.-F. Nucleic Acids Res. 2004, 32, 371-379.
19. Kumari, S.; Bugaut, A.; Huppert, J.; Balasubramanian, S. Nat. Chem. Biol. 2007, 3, 218-221.
20. Arora, A.; Dutkiewicz, M.; Scaria, V.; Hariharan, M.; Maiti, S.; Kurreck, J. RNA 2008, 14, 1290-1296.
21. Huppert, J. Chem. Soc. Rev. 2008, 37, 1375-1384.
22. Monchaud, D.; Teulade-Fichou, M.-P. Org. Biomol. Chem. 2008, 6, 627-636.
23. Kumar, N.; Patowary, A.; Sivasubbu, S.; Petersen, M.; Maiti, S. Biochemistry 2008, 47, 13179-13188.
24. Datta, B.; Armitage, B. A. J. Am. Chem. Soc. 2001, 123, 9612-9619.
25. Green, J. J.; Ying, L.; Klenerman, D.; Balasubramanian, S. J. Am. Chem. Soc. 2003, 125, 3763-3767.
26. Amato, J.; Oliviero, G.; De Pauw, E.; Gabelica, V. Biopolymers 2009, 91, 244-255.
27. Datta, B.; Schmitt, C.; Armitage, B. A. J. Am. Chem. Soc. 2003, 125, 4111-4118.
28. Roy, S.; Tanious, F.; Wilson, W. D.; Ly, D. H.; Armitage, B. A. Biochemistry 2007, 46, 10433-10443.
29. Marin, V. L.; Armitage, B. A. J. Am. Chem. Soc. 2005, 127, 8032-8033.
30. Marin, V. L.; Armitage, B. A. Biochemistry 2006, 45, 1745-1754.
31. Englund, E. A.; Xu, Q.; Witschi, M. A.; Appella, D. H. J. Am. Chem. Soc. 2006, 128, 16456-16457.
32. Paul, A.; Sengupta, P.; Krishnan, Y.; Ladame, S. Chem.-Eur. J. 2008, 14, 8682-8689.
33. Ivanova, G. D.; Arzumanov, A.; Abes, R.; Yin, H.; Wood, M. J. A.; Lebleu, B.; Gait, M. J. Nucleic Acids Res. 2008, 36, 6418-6428.
34. Koppelhus, U.; Shiraishi, T.; Zachar, V.; Pankratova, S.; Nielsen, P. E. Bioconjugate Chem. 2008, 19, 1526-1534.
35. Dragulescu-Andrasi, A.; Zhou, P.; He, G.; Ly, D. H. Chem. Commun. 2005, 244-246.
36. Zhou, P.; Wang, M.; Du, L.; Fisher, G. W.; Waggoner, A.; Ly, D. H. J. Am. Chem. Soc. 2003, 125, 6878-6879.
37. Dragulescu-Andrasi, A.; Rapireddy, S.; Frezza, B. M.; Gayathri, C.; Gil, R. R.; Ly, D. H. J. Am. Chem. Soc. 2006, 128, 10258-10267.
38. Christensen, L.; Fitzpatrick, R.; Gildea, B.; Petersen, K. H.; Hansen, H. F.; Koch, T.; Egholm, M.; Buchardt, O.; Nielsen, P. E.; Coull, J.; Berg, R. H. J. Peptide Sci. 1995, 3, 175-183.
39. Koch, T. In Peptide Nucleic Acids: Protocols and Applications, 2nd ed.; Nielsen, P. E., Ed.; Horizon Bioscience: Norfolk, 2004; pp 37-60.
40. Dawson, R. M. C. Data for Biochemical Research, 3rd ed.; Oxford University Press: New York, 1986.
41. Mergny, J.-L.; Phan, A.-T.; Lacroix, L. FEBS Lett. 1998, 435, 74-78.
42. Nguyen, B.; Tanious, F. A.; Wilson, W. D. Methods 2007, 142, 150-161.
43. Bugaut, A.; Balasubramanian, S. Biochemistry 2008, 47, 689-697.
44. Risitano, A.; Fox, K. R. Nucleic Acids Res. 2004, 32, 2598-2606.
45. Dias, N.; Sénamaud-Beaufort, C.; le Forestier, E.; Auvin, C.; Hélène, C.; Saison-Behmoaras, T. E. J. Mol. Biol. 2002, 320, 489-501.
46. Svanvik, N.; Westman, G.; Wang, D.; Kubista, M. Anal. Biochem. 2000, 281, 26-35.
47. Haq, I.; Chowdhry, B. Z.; Chaires, J. B. Eur. J. Biophys. 1997, 26, 419-426.
48. Williamson, J. R. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 703-730.
49. Ramos, A.; Hollingworth, D.; Pastore, A. RNA 2003, 9, 1198-1207.
50. Püschl, A.; Sforza, S.; Haaima, G.; Dahl, O.; Nielsen, P. E. Tetrahedron Lett. 1998, 39, 4707-4710.
51. Haaima, G.; Lohse, A.; Buchardt, O.; Nielsen, P. E. Angew. Chem., Int. Ed. 1996, 35, 1939-1942.
52. Englund, E. A.; Appella, D. H. Angew. Chem., Int. Ed. 2007, 46, 1414-1418.
53. Datta, B.; Bier, M. E.; Roy, S.; Armitage, B. A. J. Am. Chem. Soc. 2005, 127, 4199-4207.
54. Fernando, H.; Rodriguez, R.; Balasubramanian, S. Biochemistry 2008, 47, 9365-9371.
55. Schaffitzel, C.; Berger, I.; Postberg, J.; Hanes, J.; Lipps, H. J.; Plückthun, A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 8572-8577.
56. Risitano, A.; Fox, K. R. Biochemistry 2003, 42, 6507-6513.
57. Rumney, S. I.; Kool, E. T. J. Am. Chem. Soc. 1995, 117, 5635-5646.
58. McCullagh, M.; Zhang, L.; Karaba, A. H.; Zhu, H.; Schatz, G. C.; Lewis, F. D. J. Phys. Chem. B 2008, 112, 11415-11421.
59. Cevec, M.; Plavec, J. Biochemistry 2005, 44, 15238-15246.