Aminooxy functionalized oligonucleotides: Preparation, on-support derivatization, and postsynthetic attachment to polymer support

Bioconjugate Chemistry

Volumn 10, Issue 5, 1999, Pages 815-823

  Salo, Harri ^a   Virta, Pasi ^a   Hakala, Harri ^a   Prakash, Thazha P ^b   Kawasaki, Andrei M ^b   Manoharan, Muthiah ^b   Lönnberg, Harri ^a  

^a UNIVERSITY OF TURKU   (Finland)

^b ISIS PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDRAZINIUM ACETATE; IMMOBILIZATION; OLIGONUCLEOTIDE; POLYMER; PYRENE CARBALDEHYDE; PYRENE OXIME;

PYRENE;

CARBALDEHYDES; CHAIN ASSEMBLIES; CONDITION; DEPROTECTION; DERIVATIZATIONS; FUNCTIONALIZED; HYDRAZINIUM; OLIGONUCLEOTIDE SYNTHESIS; PHOSPHORAMIDITES; POLYMER SUPPORTS;

OLIGONUCLEOTIDES;

EID: 0033200125     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc990021m     Document Type: Article

References (53)

1. Gingeras, T. R., Kwoh, D. Y., and Davis, G. R. (1987) Hybridization properties of immobilized nucleic acids Nucleic Acids Res. 15, 5373-90.
2. Lund, V., Schmid, R., Rickwood, D., and Hornes, E. (1988) Assessment of methods for covalent binding of nucleic acids to magnetic beads, Dynabeads, and the characteristics of the bound nucleic acids in hybridization reactions. Nucleic Acids Res. 16, 10861-80.
3. Saiki, R. K., Walsh, P. S., Levenson, C. H., and Ehrlich, H. A. (1989) Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc. Natl. Acad. Sci. U.S.A. 86, 6230-34.
4. Albretsen, C., Kalland, K.-H., Haukanes, B.-I., Håvarstein, L.-S., and Kleppe, K. (1990) Applications of magnetic beads with covalently attached oligonucleotides in hybridization: isolation and detection of specific measles virus mRNA from a crude cell lysate. Anal. Biochem. 189, 40-50.
5. Southern, E. M., Maskos, U., and Elder, J. K. (1992) Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 13, 1008-17.
6. Williams, J. C., Case-Green, S. C., Mir, K. U., and Southern, E. M. (1994) Studies of oligonucleotide interactions by hybridization to arrays: the influence of dangling ends on duplex yield. Nucleic Acids. Res. 22, 1365-67.
7. Southern, E. M. Case-Green, S. C., Elder, J. K., Johnson, M., Mir, K. U., Wang, L., and Williams, J. C. (1994) Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res. 22, 1368-73.
8. Guo, Z., Guilfoyle, R. A., Thiel, A. J., Wang, R., and Smith, L. M. (1994) Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 22, 5456-65.
9. Stimpson, D. I., Hoijer, J. V., Hsieh, W. T., Jou, C., Gordon, J., Theriault, T., Gamble, R., and Baldeschwieler, J. D. (1995) Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical waveguides. Proc. Natl. Acad. Sci. U.S.A. 92, 6379-83.
10. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X. C., Stern, D., Winkler, J., Lockhardt, D. J., Morris, M. S., and Fodor, S. P. A. (1996) Accessing genetic information with high-density DNA arrays. Science 267, 5287.
11. Erout, M.-N., Troesch, A., Pichot, C., and Cros, P. (1996) Preparation of conjugates between oligonucleotides and N-vinylpyrrolidone/N-acryloxysuccinimide copolymers and applications in nucleic acid assays to improve sensitivity. Bioconjugate Chem. 7, 568-75.
12. O'Donnell-Maloney, M. J., Smith, C. L., and Cantor, C. R. (1996) The development of microfabricated arrays for DNA sequencing and analysis. Trends Biotechnol. 14, 401-7.
13. Yershov, G., Barsky, V., Belgovskiy, A., Kirillov, E., Kreindlin, E., Ivanov, I., Parinov, S., Gushin, D., Drobishev, A., Dubiley, S., and Mirzabekov, A. (1996) DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natl. Acad. Sci. U.S.A. 93, 4913-8.
14. Seliger, H., Bader, R., Hinz, M., Rotte, B., Astriab, A., Markiewicz, M., and Markiewicz, W. T. (1997) Synthetic oligonucleotide combinatorial libraries: tools for studying nucleic acid interactions. Nucleosides Nucleotides 16, 703-10.
15. Peterlinz, K. A., and Georgiadis, R. M. (1997) Observation of hybridization and dehybridization of thiol-tethered DNA using two-color surface plasmon resonance spectroscopy. J. Am. Chem. Soc. 119, 3401-2.
16. Pastinen, T., Kurg, A., Metspalu, A., Peltonen, L., and Syvänen, A.-C. (1997) Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7, 606-14.
17. Dubiley, S., Kirillov, E., Lysov, Y., and Mirzabekov, A. (1997) Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization. Nucleic Acids Res. 25, 2259-65.
18. Wallraff, G., Labadie, J., Brock, P., Dipietro, R., Nguyen, T., Huynh, T., Hinsberg, W., and McGall, G. (1997) DNA sequencing on a chip. Chemtech 27, 22-32.
19. Hakala, H., Mäki, E., and Lönnberg, H. (1998) Detection of oligonucleotide hybridization on a single microparticle by time-resolved fluorometry: quantitation and optimization of a sandwich type assay. Bioconjugate Chem. 9, 316-321.
20. Maskos, U., and Southern, E. M. (1992) Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesized in situ. Nucleic Acids Res. 20, 1679-84.
21. Pirrung, M. C. And Bradley, J.-C. (1995) Comparison of methods for photochemical phosphoramidite-based DNA synthesis. J. Org. Chem. 60, 6270-76.
22. Cohen, G., Deutsch, J., Fineberg, J., and Levine, A. (1997) Covalent attachment of DNA oligonucleotides to glass. Nucleic Acids Res. 25, 911-2.
23. Bader, R., Hinz, M., Schu, B., and Seliger, H. (1997) Oligonucleotide microsynthesis of a 200-mer and of one-dimensional arrays on a surface of hydroxylated polypropylene tape. Nucleosides Nucleotides 16, 829-33.
24. Weiler, J., and Hoheisel, J. D. (1997) Picomole syntheses of high quality oligonucleotide primers in combination with the preparation of oligonucleotide arrays. Nucleosides Nucleotides 16, 1793-6.
25. Hakala, H., Heinonen, P., Iitiä, A., and Lönnberg, H. (1997) Detection of oligonucleotide hybridization on a single microparticle by time-resolved fluorometry: hybridization assays on polymer particles obtained by direct solid phase assembly of the oligonucleotide probes. Bioconjugate Chem. 8, 378-84.
26. Kumar, A. (1994) Development of a suitable linkage for oligonucleotide synthesis and preliminary hybridization studies on oligonucleotides synthesized in situ. Nucleosides Nucleotides 13, 2125-34.
27. Ghosh, S., and Musso, G. (1987) Covalent attachment of oligonucleotides to solid supports. Nucleic Acids Res. 15, 5353-72.
28. Zhang, Y., Coyne, M. Y., Will, S. G., Levenson, C. H., and Kawasaki, E. S. (1991) Single-base mutational analysis of cancer and genetic diseases using membrane bound modified oligonucleotides. Nucleic Acids Res. 19, 3929-33.
29. Van Ness, J., Kalbfleisch, S., Petrie, C. R., Reed, M. W., Tabone, J. C., and Vermeulen, N. M. J. (1991) A versatile solid support system for oligodeoxynucleotide probe-based hybridization assays. Nucleic Acids Res. 19, 3345-50.
30. Timofeev, E. N., Kochetkova, S. V., Mirzabekov, A. D., and Florentiev, V. L. (1996) Regioselective immobilization of short oligonucleotides to acrylic copolymer gels. Nucleic Acids Res. 24, 3142-8.
31. Lamture, J., Beattie, K., Burke, B., Eggers, M., Ehrlich, D., Fowler, R., Hollis, M., Kosicki, B., Reich, R., Smith, S., Varma, R., and Hogan, M. (1994) Direct detection of nucleic acid hybridization on the surface of a charge coupled device. Nucleic Acids Res. 22, 2121-5.
32. Bischoff, R., Coull, J., and Regnier, F. (1987) Introduction of 5′-terminal functional groups into synthetic oligonucleotides for selective immobilization. Anal. Biochem. 164, 336-44.
33. O'Donnell, M., Tang, K., Köster, H., Smith, C., and Cantor, C. (1997) High-density, covalent attachment of DNA to silicon wafers for analysis by MALDI-TOF mass spectrometry. Anal. Chem. 69, 2438-43.
34. Kremsky, J. N., Wooter, J. L., Dougherty, J. P., Meyers, R. E., Collins, M., and Brown, E. L. (1987) Immobilization of DNA via oligonucleotides containing an aldehyde or carboxylic acid group at the 5′-terminus. Nucleic Acids Res. 15, 2891-909.
35. Hakala, H., and Lönnberg, H. (1997) Time-resolved fluorescence detection of oligonucleotide hybridization on a single microparticle: covalent immobilization of oligonucleotides and quantitation of a model system. Bioconjugate Chem. 8, 232-7.
36. Isaacs, N.(1995) Physical Organic Chemistry, 2nd ed., Longman, Essex, pp 276-7.
37. Jencks, W. P. (1964) Mechanism and catalysis of simple carbonyl group reactions. Prog. Phys. Org. Chem. 2, 63-128.
38. Karpeisky, A., Gonzalez, C., Burgin, A., B., and Beigelman, L. (1998) Highly efficient synthesis of 2′-O-amino nucleosides and their incorporation in hammerhead ribozymes. Tetrahedron Lett. 39, 1131-4.
39. Perbost, M., Hoshiko, T., Morvan, F., Swayze, E., Griffey, R., and Sanghvi, Y. (1995) Synthesis of 5′-O-amino-2′-deoxypyrimidine and purine nucleosides: building blocks for antisense oligonucleosides. J. Org. Chem. 60, 5150-6.
40. Kubo, K., Ide, H., Wallace, S. S., and Kow, Y. W. (1992) A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion. Biochemistry 31, 3703-8.
41. Ide, H., Akamatsu, K., Kimura, Y., Michiue, K., Makino, K., Asaeda, A., Takamori, Y., and Kubo, K. (1993) Synthesis and damage sensitivity of a novel probe for the detection of abasic sites of DNA. Biochemistry 32, 8276-83.
42. Boturyn, D., Boudali, A., Constant, J., Defrancq, E., and Lhomme, J. (1997) Synthesis of fluorescent probes for the detection of abasic sites in DNA. Tetrahedron 53, 5485-92.
43. Trevisiol, E., Renard, A., Defrancq, E., and Lhomme, J. (1997) The oxyamino-aldehyde coupling reaction: an efficient method for the derivatization of oligonucleotides. Tetrahedron Lett. 38, 8687-90.
44. Adarichev, V. A., Kalachikov, S. M., Kiseliova, A. V., and Dymshits, G. M. (1998) Molecular hybridization probes prepared with 4-aminooxybutylamine. Bioconjugate Chem. 9, 671-5.
45. Mitsunobu, O. (1981) The use of diethyl azodicarboxylate and triphenylphosphine in synthesis and transformation of natural products. Synthesis, 1-28.
46. Kawasaki, A. M., Casper, M. D., Prakash, T. P., Manalili, S., Sasmor, H., Manoharan, M., and Cook, P. D. (1999) Synthesis, hybridization and nuclease resistance properties of 2′-O-aminooxyethyl (2′-O-AOE) modified oligonucleotides. Tetrahedron Lett. 40, 661-4.
47. Mukkala, V.-M., Helenius, M., Hemmilä, I., Kankare, J., and Takalo, H. (1993) Development of luminescent europium-(III) and terbium(III) chelates of 2,2′:6′,2″-terpyridine derivatives for protein labeling. Helv. Chim. Acta 76, 1361-78.
48. Lövgren, T., Heinonen, P., Lehtinen, P., Hakala, H., Heinola, J., Harju, R., Takalo, H., Mukkala, V.-M., Schmid, R., Lönnberg, H., Pettersson, K., and Iitiä, A. (1997) Sensitive bioaffinity assays with individual microparticles and time-resolved fluorometry. Clin. Chem. 43, 1937-43.
49. Jones, R. A. (1984) Preparation of protected deoxyribonucleosides. In Oligonucleotide Synthesis: A Practical Approach (M. J. Gait, Ed.) p 23, IRL Press, Oxford.
50. 4-(6-amino-hexyl)-2′-deoxy-5′-O-(4, 4′-dimethoxytrityl)cytidine. Nucleosides, Nucleotides 17, 1209-13.
51. Azhayev, A., Guzaev, A., Hovinen, J., Azhayeva, E., and Lönnberg, H. (1993) Analogues of oligonucleotides containing 3′-deoxy-β-D-psicothymidine. Tetrahedron Lett. 34, 6435-8.
52. Kahl, J. D., and Greenberg, M. M. (1999) Introducing structural diversity in oligonucleotides via photolabile, convertible C5-substituted nucleotides. J. Am. Chem. Soc. 121, 597-604.
53. Kahl, J. D., McMinn, D. L., and Greenberg, M. M. (1998) High-yielding method for on-column derivatization of protected oligodeoxynucleotides and its application to the convergent synthesis of 5′,3′-bis-conjugates. J. Org. Chem. 63, 4870-1.