Hybridization of complementary and homologous peptide nucleic acid oligomers to a guanine quadraplex-forming RNA

Biochemistry

Volumn 45, Issue 6, 2006, Pages 1745-1754

  Marin, Violeta L ^a   Armitage, Brace A ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENCE; OLIGOMERS; RNA; SPECTROSCOPIC ANALYSIS; THERMODYNAMIC PROPERTIES; ULTRAVIOLET RADIATION;

PEPTIDE NUCLEIC ACID (PNA); PNA-RNA QUADRUPLEXES; WATSON-CRICK BASE PAIRS;

PROTEINS;

GUANINE; PEPTIDE NUCLEIC ACID; RNA;

ARTICLE; BASE PAIRING; CIRCULAR DICHROISM; FLUORESCENCE SPECTROSCOPY; GENETIC COMPLEMENTATION; HYBRIDIZATION; HYDROGEN BOND; MOLECULAR RECOGNITION; NONHUMAN; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN RNA BINDING; SPECTROFLUOROMETRY;

ANIMALS; BASE SEQUENCE; CIRCULAR DICHROISM; CYTOSINE; GUANINE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; PEPTIDE NUCLEIC ACIDS; RNA; SPECTROPHOTOMETRY, ULTRAVIOLET; TEMPERATURE;

EID: 32344449024     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi051831q     Document Type: Article

References (59)

1. Williamson, J. R. (1994) G-quartet structures in telomeric DNA, Annu. Rev. Biophys. Biomol. Struct. 23, 703-730.
2. Simonsson, T. (2001) G-quadruplex DNA structures-Variations on a theme, Biol. Chem. 382, 621-628.
3. Davis, J. T. (2004) G-quartets 40 years later: From 5′-GMP to molecular biology and supramolecular chemistry, Angew. Chem. Int. Ed. 43, 668-698.
4. Kumar, N., and Maiti, S. (2004) Quadruplex to Watson-Crick duplex transition of the thrombin binding aptamer. A fluorescence resonance energy transfer study, Biochem. Biophys. Res. Comm. 319, 759-767.
5. Williamson, J. R., Raghuraman, M. K., and Cech, T. R. (1989) Monovalent cation-induced structure of telomeric DNA: The G-quartet model, Cell 59, 871-880.
6. Shafer, R. H., and Smirnov, I. (2001) Biological aspects of DNA/RNA quadruplexes, Biopolymers 56, 209-227.
7. Catasti, P., Chen, X., Moyzis, R. K., Bradbury, E. M., and Gupta, G. (1996) Structure-function correlations of the insulin-linked polymorphic region, J. Mol. Biol. 264, 534-545.
8. Simonsson, T., Pecinka, P., and Kubista, M. (1998) DNA tetraplex formation in the control region of c-myc, Nucleic Acids Res. 26, 1167-1172.
9. Siddiqui-Jain, A., Grand, C. L., Bearss, D. J., and Hurley, L. H. (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription, Proc. Nad. Acad. Sci. U.S.A. 99, 11593-11598.
10. Frantz, J. D., and Gilbert, W. (1995) A novel yeast gene product, G4p1, with a specific affinity for quadruplex nucleic acids, J. Biol. Chem. 270, 20692-20697.
11. Schaeffer, C., Bardoni, B., Mandel, J.-L., Ehresmann, B., Ehresmann, C., and Moine, H. (2001) The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif, EMBO J. 20, 4803-4813.
12. Darnell, J. C., Jensen, K. B., Jin, P., Brown, V., Warren, S. T., and Darnell, R. B. (2001) Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function, Cell 107, 489-499.
13. Brown, V., Jin, P., Ceman, S., Darnell, J. C., O'Donnell, W. T., Tenenbaum, S. A., Jin, X., Feng, Y., Wilkinson, K. D., Keene, J. D., Darnell, R. B., and Warren, S. T. (2001) Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in Fragile X syndrome, Cell 107, 477-487.
14. Ramos, A., Hollingworth, D., and Pastore, A. (2003) G-quartet-dependent recognition between the FMRP RGG box and RNA, RNA 9, 1198-1207.
15. Sirand-Pugnet, P., Durosay, P., Brody, E., and Marie, J. (1995) An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken β-tropomyosin pre-mRNA, Nucleic Acids Res. 23, 3501-3507.
16. Gomez, D., Lemarteleur, T., Lacroix, L., Mailliet, P., Mergny, J.-L., and Riou, J.-F. (2004) Telomerase downregulation induced by the G-quadruplex ligand 12459 in A549 cells is mediated by hTERT RNA alternative splicing, Nucleic Acids Res. 32, 371-379.
17. Bonnal, S., Schaeffer, C., Créancier, L., Clamens, S., Moine, H., Prats, A.-C., and Vagner, S. (2003) A single internal ribosome entry site containing a G quartet RNA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons, J. Biol. Chem. 278, 39330-39336.
18. Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H., and Toole, J. J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin, Nature 355, 564-566.
19. Macaya, R. F., Schultze, P., Smith, F. W., Roe, J. A., and Feigon, J. (1993) Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution, Proc. Natl. Acad. Sci. U.S.A. 90, 3745-3749.
20. Wang, K. Y., McCurdy, S., Shea, R. G., Swaminathan, S., and Bolton, P. H. (1993) A DNA aptamer which binds to and inhibits thrombin exhibits a new structural motif for DNA, Biochemistry 32, 1899-1904.
21. Wen, J.-D., Gray, C. W., and Gray, D. M. (2001) SELEX selection of high-affinity oligonucleotides for bacteriophage Ff gene 5 protein, Biochemistry 40, 9300-9310.
22. Andreola, M.-L., Pileur, F., Calmels, C., Ventura, M., Tarrago-Litvak, L., Toulmé, J.-J., and Litvak, S. (2001) DNA aptamers selected against the HIV-1 RNase H display in vitro antiviral activity, Biochemistry 40, 10087-10094.
23. Mori, T., Oguro, A., Ohtsu, T., and Nakamura, Y. (2004) RNA aptamers selected against the receptor activator of NF-kB acquire general affinity to proteins of the tumor necrosis factor receptor family, Nucleic Acids Res. 32, 6120-6128.
24. Cuesta, J., Read, M. A., and Neidle, S. (2003) The design of G-quadruplex ligands as telomerase inhibitors, Mini-Rev. Med. Chem. 3, 11-21.
25. Seenisamy, J., Bashyam, S., Gokhale, V., Vankayalapati, H., Sun, D., Siddiqui-Jain, A., Streiner, N., Shin-ya, K., White, E., Wilson, W. D., and Hurley, L. H. (2005) Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure, J. Am. Chem. Soc. 127, 2944-2959.
26. Rezler, E. M., Seenisamy, J., Bashyam, S., Kim, M.-Y., White, E., Wilson, W. D., and Hurley, L. H. (2005) Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure, J. Am. Chem. Soc. 127, 9439-9447.
27. Datta, B., and Armitage, B. A. (2001) Hybridization of PNA to structured DNA targets: Quadruplex invasion and the overhang effect, J. Am. Chem. Soc. 123, 9612-9619.
28. Green, J. J., Ying, L., Klenerman, D., and Balasubramanian, S. (2003) Kinetics of unfolding the human telomeric DNA quadruplex using a PNA trap, J. Am. Chem. Soc. 125, 3763-3767.
29. Marin, V. L., and Armitage, B. A. (2005) RNA guanine quadruplex invasion by complementary and homologous PNA probes, J. Am. Chem. Soc. 127, 8032-8033.
30. 2 hybrid quadruplex, J. Am. Chem. Soc. 125, 4111-4118.
31. Dawson, R. M. C., Elliott, D. C., Elliott, W. H., and Jones, K. M. (1986) in Data for Biochemical Research, pp 103-114, Oxford University Press, New York.
32. Christensen, L., Fitzpatrick, R., Gildea, B., Petersen, K. H., Hansen, H. F., Koch, T., Egholm, M., Buchardt, O., Nielsen, P. E., Coull, J., and Berg, R. H. (1995) Solid-phase synthesis of peptide nucleic acids, J. Peptide Sci. 3, 175-183.
33. Koch, T. (2004) in Peptide Nucleic Acids: Protocols and Applications (Nielsen, P. E., Ed.) pp 37-60, Horizon Bioscience, Norfolk, U.K.
34. Zhou, X.-f., Peng, Z.-h., Geise, J., Peng, B.-x., Li, Z.-x., Yan, M., Domisse, R., Carieer, R., and Claeys, M. (1995) Blue sensitizing dyes: Synthesis, spectroscopy, and performance in photographic emulsions, J. Imaging Sci. Technol. 39, 244-252.
35. Svanvik, N., Westman, G., Wang, D., and Kubista, M. (2000) Light-up probes: Thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution, Anal. Biochem. 281, 26-35.
36. van Holde, K. E., Johnson, C. W., and Ho, P. S. (1998) in Principles of Physical Biochemistry, p 657, Prentice Hall, Upper Saddle River, NJ.
37. Job, P. (1928) Recherches sur la formation de complexes minéraux en solution, et sur leur stabilité, Ann. Chim. 9, 113-203.
38. Dias, N., Sénamaud-Beaufort, C., le Forestier, E., Auvin, C., Hélène, C., and Saison-Behmoaras, T. E. (2002) RNA hairpin invasion and ribosome elongation arrest by mixed base PNA oligomer, J. Mol. Biol. 320, 489-501.
39. Gray, D. M., Tinoco, I. J., and Chamberlin, M. J. (1972) The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation, Biopolymers 11, 1235-1258.
40. Mergny, J.-L., Phan, A.-T., and Lacroix, L. (1998) Following G-quartet formation by UV-spectroscopy, FEBS Lett. 435, 74-78.
41. Marky, L. A., and Breslauer, K. J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves, Biopolymers 26, 1601-1620.
42. Egholm, M., Buchardt, O., Christensen, L., Behrens, C., Freier, S. M., Driver, D. A., Berg, R. H., Kim, S. K., Nordén, B., and Nielsen, P. E. (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules, Nature 365, 566-568.
43. Lee, L. G., Chen, C., and Liu, L. A. (1986) Thiazole orange: A new dye for reticulocyte analysis, Cytometry 7, 508-517.
44. Nygren, J., Svanvik, N., and Kubista, M. (1998) The interactions between the fluorescent dye thiazole orange and DNA, Biopolymers 46, 39-51.
45. Rye, H. S., Yue, S., Wemmer, D. E., Quesada, M. A., Haugland, R. P., Mathies, R. A., and Glazer, A. N. (1992) Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: Properties and applications, Nucleic Acids Res. 20, 2803-2812.
46. Netzel, T. L., Nafisi, K., Zhao, M., Lenhard, J. R., and Johnson, I. (1995) Base-content dependence of emission enhancements, quantum yields, and lifetimes for cyanine dyes bound to double-stranded DNA: photophysical properties of monomeric and bichromophoric DNA stains, J. Phys. Chem. 99, 17936-17947.
47. Ishiguro, T., Saitoh, J., Yawata, H., Otsuka, M., Inoue, T., and Sugiura, Y. (1996) Fluorescence detection of specific sequence of nucleic acids by oxazole yellow-linked oligonucleotides. Homogeneous quantitative monitoring of in vivo transcription, Nucleic Acids Res. 24, 4992-4997.
48. 4 quadruplex, J. Am. Chem. Soc. 126, 5944-5945.
49. Datta, B., Bier, M. E., Roy, S., and Armitage, B. A. (2005) Quadruplex formation by a guanine-rich PNA oligomer, J. Am. Chem. Soc. 127, 4199-4207.
50. Svanvik, N., Nygren, J., Westman, G., and Kubista, M. (2001) Free-probe fluorescence of light-up probes, J. Am. Chem. Soc. 123, 803-809.
51. Smirnov, I., and Shafer, R. F. (2000) Effect of loop sequence and size on DNA aptamer stability, Biochemistry 39, 1462-1468.
52. Seenisamy, J., Rezler, E. M., Powell, T. J., Tye, D., Gokhale, V., Joshi, C. S., Siddiqui-Jain, A., and Hurley, L. H. (2004) The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4, J. Am. Chem. Soc. 126, 8702-8709.
53. Phan, A. T., Modi, Y. S., and Patel, D. J. (2004) Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter, J. Am. Chem. Soc. 8710-8716.
54. Oliver, A. W., and Kneale, G. G. (1999) Structural characterization of DNA and RNA sequences recognized by the gene 5 protein of bacteriophage fd, Biochem. J. 339, 525-531.
55. Dapic, V., Abdomerovic, V., Marrington, R., Peberdy, J., Rodger, A., Trent, J. O., and Bates, P. J. (2003) Biophysical and biological properties of quadruplex oligodeoxyribonucleotides, Nucleic Acids Res. 31, 2097-2107.
56. Risitano, A., and Fox, K. R. (2004) Influence of loop size on the stability of intramolecular DNA quadruplexes, Nucleic Acids Res. 32, 2598-2606.
57. Hazel, P., Huppert, J., Balasubramanian, S., and Neidle, S. (2004) Loop-length-dependent folding of G-quadruplexes, J. Am. Chem. Soc. 126, 16405-16415.
58. Griffith, M. C., Risen, L. M., Greig, M. J., Lesnik, E. A., Sprankle, K. G., Griffey, R. H., Kiely, J. S., and Freier, S. M. (1995) Single and bis peptide nucleic acids as triplexing agents: Binding and stoichiometry, J. Am. Chem. Soc. 117, 831-832.
59. Lesnik, E. A., Risen, L. M., Driver, D. A., Griffith, M. C., Sprankle, K., and Freier, S. M. (1997) Evaluation of pyrimidine PNA binding to ssDNA targets from nonequilibrium melting experiments, Nucleic Acids Res. 25, 568-574.