G-quadruplex-forming oligonucleotide conjugated to magnetic nanoparticles: Synthesis, characterization, and enzymatic stability assays

Bioconjugate Chemistry

Volumn 23, Issue 3, 2012, Pages 382-391

  Musumeci, Domenica ^a,b   Oliviero, Giorgia ^a   Roviello, Giovanni N ^b   Bucci, Enrico M ^b   Piccialli, Gennaro ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BINARY ALLOYS; ELECTROPHORESIS; ENZYMES; FLUORESCENCE; MAGNETITE; MAGNETITE NANOPARTICLES; NANOMAGNETICS; STABILITY; SYNTHESIS (CHEMICAL);

APTAMERS; CONDITION; ENZYMATIC STABILITY; G-QUADRUPLEXES; GUANINE; OPTICAL SPECTROSCOPY; QUADRUPLE HELICES; SUPERPARAMAGNETIC NANOPARTICLES; THROMBIN BINDING; UNIMOLECULAR;

OLIGONUCLEOTIDES;

APTAMER; FLUORESCENT DYE; OLIGODEOXYRIBONUCLEOTIDE; OLIGODEOXYRIBONUCLEOTIDE SUPERPARAMAGNETIC IRON OXIDE NANOPARTICLE CONJUGATE; SUPERPARAMAGNETIC IRON OXIDE NANOPARTICLE; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; DRUG CONJUGATION; DRUG STABILITY; DRUG SYNTHESIS; ELECTROPHORESIS; ELECTROSPRAY MASS SPECTROMETRY; FLUORESCENCE SPECTROSCOPY; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ULTRAVIOLET SPECTROSCOPY;

EID: 84858715991     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc200305t     Document Type: Article

References (56)

1. Gupta, A. K. and Gupta, M. (2005) Synthesis and surface engineering of iron oxide nanoparticles for biomedical applications Biomaterials 26, 3995-4021 (Pubitemid 40044762)
2. Laurent, S., Forge, D., Port, M., Roch, A., Robic, C., Vander Elst, L., and Muller, R. N. (2008) Magnetic iron oxide nanoparticles: synthesis, stabilization, vectorization, physicochemical characterizations, and biological applications Chem. Rev. 108, 2064-2110
3. Gao, J., Gu, H., and Xu, B. (2009) Multifunctional magnetic nanoparticles: design, synthesis, and biomedical applications Acc. Chem. Res. 42, 1097-1107
4. Mahmoudi, M., Stroeve, P., Milani, A. S., and Arbab, A. S. (2011) Superparamagnetic Iron Oxide Nanoparticles: Synthesis, Surface Engineering, Cytotoxicity and Biomedical Applications, Nova Science Pub Inc.
5. Yang, H. H., Zhang, S. Q., Chen, X. L., Zhuang, Z. X., Xu, J. G., and Wang, X. R. (2004) Magnetite-containing spherical silica nanoparticles for biocatalysis and bioseparations Anal. Chem. 76, 1316-21
6. Berensmeier, S. (2006) Magnetic particles for the separation and purification of nucleic acids Appl. Microbiol. Biotechnol. 73, 495-504 (Pubitemid 350262626)
7. Takeda, S., Terazono, B., Mishima, F., Nakagami, H., Nishijima, S., and Kaneda, Y. (2006) Novel drug delivery system by surface modified magnetic nanoparticles J. Nanosci. Nanotechnol. 6, 3269-76 (Pubitemid 44580010)
8. Arruebo, M., Fernandez-Pacheco, R., Ibarra, M. R., and Santamaria, J. (2007) Magnetic nanoparticles for drug delivery Nano Today 2 (3) 22-32 (Pubitemid 46695431)
9. Hanessian, S., Grzyb, J. A., Cengelli, F., and Juillerat-Jeanneret, L. (2008) Synthesis of chemically functionalized superparamagnetic nanoparticles as delivery vectors for chemotherapeutic drugs Bioorg. Med. Chem. 16, 2921-31 (Pubitemid 351418211)
10. Williams, P. S., Carpino, F., and Zborowski, M. (2009) Magnetic nanoparticle drug carriers and their study by quadrupole magnetic field-flow fractionation Mol. Pharmaceutics 6, 1290-306
11. Thorek, D. L., Chen, A. K., Czupryna, J., and Tsourkas, A. (2006) Superparamagnetic iron oxide nanoparticle probes for molecular imaging Ann. Biomed. Eng. 34, 23-38
12. Duguet, E., Vasseur, S., Mornet, S., and Devoisselle, J. M. (2006) Magnetic nanoparticles and their applications in medicine Nanomedicine 1 (2) 157-68
13. Peng, X. H., Qian, X., Mao, H., Wang, A. Y., Chen, Z. G., Nie, S., and Shin, D. M. (2008) Targeted magnetic iron oxide nanoparticles for tumor imaging and therapy Int. J. Nanomedicine 3, 311-21
14. Laurent, S., Boutry, S., Mahieu, I., Vander Elst, L., and Muller, R. N. (2009) Iron oxide based MR contrast agents: from chemistry to cell labeling Curr. Med. Chem. 16 (35) 4712-4727
15. Plank, C., Schillinger, U., Scherer, F., Bergemann, C., Remy, J. S., Kroetz, F., Anton, M., Lausier, J., and Rosenecker, J. (2003) The magnetofection method: using magnetic force to enhance gene delivery J. Biol. Chem. 384, 737-747 (Pubitemid 36747935)
16. Schillinger, U., Brill, T., Rudolph, C., Huth, S., Gersting, S., Krötz, F., Hirschberger, J., Bergemann, C., and Plank, C. (2005) Advances in magnetofection-magnetically guided nucleic acid delivery J. Magn. Magn. Mater. 293, 501-508 (Pubitemid 40608971)
17. Kamau, S. W., Hassa, P. O., Steitz, B., Petri-Fink, A., Hofmann, H., Hofmann-Amtenbrink, M., von Rechenberg, B., and Hottiger, M. O. (2006) Enhancement of the efficiency of non-viral gene delivery by application of pulsed magnetic field Nucl. Acid Res. 34 (5) e40
18. Chorny, M., Polyak, B., Alferiev, I. S., Walsh, K., Friedman, G., and Levy, R. J. (2007) Magnetically driven plasmid DNA delivery with biodegradable polymeric nanoparticles FASEB J. 21, 2510-2519 (Pubitemid 47230680)
19. Yang, S. Y., Sun, J. S., Liu, C. H., Tsuang, Y. H., Chen, L. T., Hong, C. Y., Yang, H. C., and Horng, H. E. (2008) Ex vivo magnetofection with magnetic nanoparticles: a novel platform for nonviral tissue engineering Artif. Organs 32, 195-204
20. McBain, S. C., Griesenbach, U., Xenariou, S., Keramane, A., Batich, C. D., Alton, E. W. F. W., and Dobson, J. (2008) Magnetic nanoparticles as gene delivery agents: enhanced transfection in the presence of oscillating magnet arrays Nanotechnology 19, 405102
21. Pino, P., Munoz-Javier, A., Vlaskou, D., Rivera Gil, P., Plank, C., and Parak, W. J. (2010) Gene silencing mediated by magnetic lipospheres tagged with small interfering RNA Nano Lett. 10, 3914-3921
22. Gupta, A. K., Naregalkar, R. R., Vaidya, V. D., and Gupta, M. (2007) Recent advances on surface engineering of magnetic iron oxide nanoparticles and their biomedical applications Nanomedicine 2, 23-39 (Pubitemid 46845774)
23. Kettering, M., Winter, J., Zeisberger, M., Bremer-Streck, S., Oehring, H., Bergemann, C., Alexiou, C., Hergt, R., Halbhuber, K. J., Kaiser, W. A., and Hilger, I. (2007) Magnetic nanoparticles as bimodal tools in magnetically induced labelling and magnetic heating of tumour cells: an in vitro study Nanotechnology 18, 1-9
24. Xu, C. and Sun, S. (2009) Superparamagnetic nanoparticles as targeted probes for diagnostic and therapeutic applications Dalton Trans. 29, 5583-5591
25. Chen, B., Wu, W., and Wang, X. (2011) Magnetic iron oxide nanoparticles for tumor-targeted therapy Curr. Cancer Drug Targets 11, 184-9
26. Lu, A. H., Salabas, E. L., and Schüth, F. (2007) Magnetic nanoparticles: synthesis, protection, functionalization, and application Angew. Chem., Int. Ed. Engl. 46, 1222-44
27. Seo, Y. J., Lee, I. J., Yi, J. W., and Kim, B. H. (2007) Probing the stable G-quadruplex transition using quencher-free end-stacking ethynyl pyrene-adenosine Chem. Commun. 2817-2819 (Pubitemid 47035574)
28. Seo, Y. J., Lee, I. J., and Kim, B. H. (2008) Detection of structure-switching in G-quadruplexes using end-stacking ability Bioorg. Med. Chem. Lett. 18, 3910-3913
29. Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H., and Toole, J. J. (1992) Selection of sinlge-stranded DNA molecules that bind and inhibit human thrombin Nature 355, 564-566
30. 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 (Pubitemid 23111444)
31. 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 (Pubitemid 23086037)
32. Padmanabhan, K., Padmanabhan, K. P., Ferrara, J. D., Sadler, J. E., and Tulinsky, A. (1993) The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer J. Biol. Chem. 268, 17651-17654 (Pubitemid 23260263)
33. Schultze, P., Macaya, R. F., and Feigon, J. (1994) Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) J. Mol. Biol. 235, 1532-1547 (Pubitemid 24150403)
34. Wang, K. Y., Krawczyk, S. H., Bischofberger, N., Swaminathan, S., and Bolton, P. H. (1993) The tertiary structure of a DNA aptamer which binds to and inhibits thrombin determines activity Biochemistry 32, 11285-11292 (Pubitemid 23332039)
35. Smirnov, I. and Shafer, R. H. (2000) Effect of loop sequence and size on DNA aptamer stability Biochemistry 39, 1462-1468 (Pubitemid 30090716)
36. Sacca, B., Lacroix, L., and Mergny, J.-L. (2005) The effect of chemical modifications on the thermal stability of different G-quadruplex-forming oligonucleotides Nucleic Acids Res. 33, 1182-1192 (Pubitemid 41439911)
37. Tang, C.-F. and Shafer, R. H. (2006) Engineering the quadruplex fold: nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes J. Am. Chem. Soc. 128, 5966-5973 (Pubitemid 43724394)
38. Martino, L., Virno, A., Randazzo, A., Virgilio, A., Esposito, V., Giancola, C., Bucci, M., Cirino, G., and Mayol, L. (2006) A new modified thrombin binding aptamer containing a 5′-5′ inversion of polarity site Nucleic Acids Res. 34, 6653-6662 (Pubitemid 46019401)
39. Virno, A., Randazzo, A., Giancola, C., Bucci, M., Cirino, G., and Mayol, L. (2007) A novel thrombin binding aptamer containing a G-LNA residue Bioorg. Med. Chem. 15, 5710-5718 (Pubitemid 47043478)
40. Pagano, B., Martino, L., Randazzo, A., and Giancola, C. (2008) Stability and binding properties of a modified thrombin binding aptamer Biophys. J. 94, 562-569
41. Nallagatla, S. R., Heuberger, B., Haque, A., and Switzer, C. (2009) Combinatorial synthesis of thrombin-binding aptamers containing iso-guanine J. Comb. Chem. 11, 364-369
42. Russo Krauss, I., Merlino, A., Giancola, C., Randazzo, A., Mazzarella, L., and Sica, F. (2011) Thrombin-aptamer recognition: a revealed ambiguity Nucleic Acids Res. 39, 7858-67
43. Coppolla, T., Varra, M., Oliviero, G., Galeone, A., D'Isa, G., Mayol, L., Morelli, E., Bucci, M. R., Vallecco, V., Cirino, G., and Borbone, N. (2008) Synthesis, structural studies and biological properties of new TBA analogues containing acyclic nucleotide Bioorg. Med. Chem. 16, 8244-8253
44. Raviv, S. M., Horvath, A., Aradi, J., Bagoly, Z., Fazakas, F., Batta, Z., Muszbek, L., and Harsfalvi, J. (2008) 4-Thio-deoxyuridylate-modified thrombin aptamer and its inhibitory effect on fibrin clot formation, platelet aggregation and thrombus growth on subendothelial matrix J. Thromb. Homeost. 6, 1764-1771
45. Bonifacio, L., Church, F., and Jarstfer, M. (2008) Effect of locked-nucleic acid on a biologically active G-quadruplex. A structure-activity relationship of the thrombin aptamer Int. J. Mol. Sci. 9, 422-433 (Pubitemid 351482125)
46. Pasternak, A., Hernandez, F. J., Rasmussen, L. M., Vester, B., and Wengel, J. (2011) Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer Nucleic Acids Res. 39, 1155-64
47. Nagatoishi, S., Nojima, T., Juskowiak, B., and Takenaka, S. (2005) A Pyrene-labeled Gquadruplexoligonucleotide as a fluorescent probe for potassium ion detection in biological applications Angew. Chem., Int. Ed. 44, 5067-5070 (Pubitemid 41188545)
48. Nagatoishi, S., Nojima, T., Galezowska, E., Juskowiak, B., and Takenaka, S. (2006) G quadruplex-based FRET probes with the thrombin-binding aptamer (TBA) sequence designed for the efficient fluorometric detection of the potassium Ion ChemBioChem 7, 1730-1737 (Pubitemid 44748657)
49. Cavaluzzi, J. M. and Borer, P. N. (2004) Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA Nucleic Acids Res. 32 (1) e13 10.1093/nar/gnh015
50. Mergny, J. L., Phan, A. T., and Lacroix, L. (1998) Following G-quartet formation by UV-spectroscopy FEBS Lett. 435, 74-78 (Pubitemid 28432018)
51. Nagao, D., Yokoyama, M., Yamauchi, N., Matsumoto, H., Kobayashi, Y., and Konno, M. (2008) Synthesis of highly monodisperse particles composed of a magnetic core and fluorescent shell Langmuir 24, 9804-9808
52. Kankia, B. I. (2004) Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids Nucleic Acids Res. 32 (19) e154
53. Seo, Y. J. and Kim, B. H. (2006) Probing the B-to-Z-DNA duplex transition using terminally stacking ethynyl pyrene-modified adenosine and uridine bases Chem. Commun. 150-152
54. Seferos, D. S., Prigodich, A. E., Giljohann, D. A., Patel, P. C., and Mirkin, C. A. (2009) Polyvalent DNA nanoparticle conjugates stabilize nucleic acids Nano Lett. 9, 308-311
55. Milano, G., Musumeci, D., Gaglione, M., and Messere, A. (2010) An alternative strategy to synthesize PNA and DNA magnetic conjugates forming nanoparticle assembly based on PNA/DNA duplexes Mol. BioSyst. 6, 553-61
56. Song, G., Chen, M., Chen, C., Wang, C., Hu, D., Ren, J., and Qu, X. (2010) Design of proton-fueled tweezers for controlled, multi-function DNA-based molecular device Biochimie 92, 121-127