Azide - Alkyne "click" conjugation of 8-aza-7-deazaadenine-DNA: Synthesis, duplex stability, and fluorogenic dye labeling

Bioconjugate Chemistry

Volumn 21, Issue 9, 2010, Pages 1629-1641

  Seela, Frank ^a   Pujari, Suresh S ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

1 [2 DEOXY 3,5 DI O (4 TOLUOYL) BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 (OCTA 1,7 DIYNYL) 4 METHOXY 1H PYRAZOLO[3,4 D]PYRIMIDINE; 1 [2 DEOXY 5 O (4,4 DIMETHOXYTRITYL) BETA DEXTRO ERYTHROPENTO FURANOSYL] 4 [[(N,N DIMETHYLAMINO)METHYLIDENE]AMINO] 3 (OCTA 1,7 DIYNYL) 1H PYRAZOLO[3,4 D]PYRIMIDIN 3' (2 CYANOETHYL) N,N DIISOPROPYLPHOSPHORAMIDITE; 1 [2 DEOXY 5 O (4,4' DIMETHOXYTRITYL) BETA DEXRO ERYTHROPENTOFURANOSYL] 4 [[(N,N DIMETHYLAMINO)METHYLIDENE]AMINO] 3 (OCTA 1,7 DIYNYL) 1H PYRAZOLO[3,4 D]PYRIMIDINE; 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 (OCTA 1,7 DIYNYL) 1H PYRAZOLO[3,4 D]PYRIMIDIN 4 AMINE; 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 (OCTA 1,7 DIYNYL) 4 METHOXY 1H PYRAZOLO[3,4 D]PYRIMIDINE; 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 (OCTA 1,7 DIYNYL) 4 [[(N,N DIMETHYLAMINO)METHYLIDENE]]AMINO 1H PYRAZOLO[3,4 D]PYRIMIDINE; 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 IODO 1H PYRAZOLO[3,4 D]PYRIMIDIN 4 AMINE; 3 AZIDO 7 HYDROXYCOUMARIN; 4 AMINO 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 [(7 HYDROXYCOUMARIN 1',2',3' TRIAZOL 4' YL)HEXYLIDYNE] 1H PYRAZOLO[3,4 D]PYRIMIDINE; 4 AMINO 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 [(BENZYL 1',2',3' TRIAZOL 4' YL)HEXYLIDYNE] 1H PYRAZOLO[3,4 D]PYRIMIDINE; 4 AMINO 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 [(METHYLANTHRACENE 1',2',3' TRIAZOL 4' YL)HEXYLIDYNE] 1H PYRAZOLO[3,4 D]PYRIMIDINE; 4 AMINO 1 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 3 [[(1,2,3,4 TETRAHYDRO 5 METHYL 2,4 DIOXOPYRIMIDIN 1 YL)FURAN 3 YL] (1,2,3 TRIAZOL 4' YL)HEXYLIDYNE] 1H PYRAZOLO[3,4 D]PYRIMIDINE; 4 AMINO 7 [2 DEOXY BETA DEXTRO ERYTHROPENTOFURANOSYL] 5 [(METHYLANTHRACEN 1',2',3' TRIAZOL 4' YL)HEXYLIDYNE] 7H PYRROLO[2,3 D]PYRIMIDINE; 8 AZA 7 DEAZAADENINE; 9 AZIDOMETHYL ANTHRACENE; ADENINE DERIVATIVE; ALKYNE DERIVATIVE; ANTHRACENE DERIVATIVE; AZIDE; COUMARIN DERIVATIVE; PYRIMIDINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL REACTION; CHEMICAL STRUCTURE; CONJUGATION; DNA STRAND; PRIMED IN SITU LABELING; PROTON NUCLEAR MAGNETIC RESONANCE; SYNTHESIS;

EID: 77956621001     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc100090y     Document Type: Article

References (60)

1. Kobayashi, H., Ogawa, M., Alford, R., Choyke, P. L., and Urano, Y. (2010) New strategies for fluorescent probe design in medical diagnostic imaging. Chem. Rev. DOI: 10.1021/cr900263j.
2. Hrdlicka, P. J., Babu, B. R., Sørensen, M. D., Harrit, N., and Wengel, J. (2005) Multilabeled pyrene-functionalized 2′-amino-LNA probes for nucleic acid detection in homogeneous fluorescence assays J. Am. Chem. Soc. 127, 13293-13299
3. Astakhova, I. V., Korshun, V. A., Jahn, K., Kjems, J., and Wengel, J. (2008) Perylene attached to 2′-amino-LNA: Synthesis, incorporation into oligonucleotides, and remarkable fluorescence properties in vitro and in cell culture Bioconjugate Chem. 19, 1995-2007
4. Marti, A. A., Jockusch, S., Stevens, N., Ju, J., and Turro, N. J. (2007) Fluorescent hybridization probes for sensitive and selective DNA and RNA detection Acc. Chem. Res. 40, 402-409
5. 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, 232-237
6. Cuppoletti, A., Cho, Y., Park, J.-S., Strässler, C., and Kool, E. T. (2005) Oligomeric fluorescent labels for DNA Bioconjugate Chem. 16, 528-534
7. Droumaguet, C. L., Wang, C., and Wang, Q. (2010) Fluorogenic click reaction. Chem. Soc. Rev. DOI: 10.1039/b901975h.
8. Best, M. D. (2009) Click chemistry and bioorthogonal reactions: Unprecedented selectivity in the labeling of biological molecules Biochemistry 48, 6571-6584
9. Huisgen, R. (1989) Kinetics and reaction mechanisms: Selected examples from the experience of forty years Pure Appl. Chem. 61, 613-628
10. Huisgen, R., Szeimies, G., and Moebius, L. (1967) Kinetik der Additionen organischer Azide an CC-Mehrfachbindungen Chem. Ber. 100, 2494-2507
11. Meldal, M. and Tornøe, C. W. (2008) Cu-catalyzed azide-alkyne cycloaddition Chem. Rev. 108, 2952-3015
12. Tornøe, C. W., Christensen, C., and Meldal, M. (2002) Peptidotriazoles on solid phase: [1,2,3]-Triazoles by regiospecific copper(I)-catalyzed 1,3- dipolar cycloadditions of terminal alkynes to azides J. Org. Chem. 67, 3057-3064
13. Rostovtsev, V. V., Green, L. G., Fokin, V. V., and Sharpless, K. B. (2002) A stepwise Huisgen cycloaddition process: Copper (I)-catalyzed regioselective "ligation" of azides and terminal alkynes Angew. Chem., Int. Ed. 41, 2596-2599
14. Seela, F., Sirivolu, V. R., and Chittepu, P. (2008) Modification of DNA with octadiynyl side chains: Synthesis, base pairing, and formation of fluorescent coumarin dye conjugates of four nucleobases by the alkyne-azide "click" reaction Bioconjugate Chem. 19, 211-224
15. Gramlich, P. M. E., Wirges, C. T., Manetto, A., and Carell, T. (2008) Postsynthetic DNA modification through the copper-catalyzed azide-alkyne cycloaddition reaction Angew. Chem., Int. Ed. 47, 8350-8358
16. Kocalka, P., El-Sagheer, A. H., and Brown, T. (2008) Rapid and efficient DNA strand cross-linking by click chemistry ChemBioChem 9, 1280-1285
17. Hotha, S. and Kashyap, S. (2006) "Click chemistry" inspired synthesis of pseudo -oligosaccharides and amino acid glycoconjugates J. Org. Chem. 71, 364-367
18. Seela, F., Xiong, H., Leonard, P., and Budow, S. (2009) 8-Aza-7-deazaguanine nucleosides and oligonucleotides with octadiynyl side chains: Synthesis, functionalization by the azide-alkyne 'click' reaction and nucleobase specific fluorescence quenching of coumarin dye conjugates Org. Biomol. Chem. 7, 1374-1387
19. Sirivolu, V. R., Chittepu, P., and Seela, F. (2008) DNA with branched internal side chains: Synthesis of 5-tripropargylamine-dU and conjugation by an azide-alkyne double click reaction ChemBioChem 9, 2305-2316
20. Agnew, B., Buck, S., Nyberg, T., Bradford, J., Clarke, S., and Gee, K. (2008) Click chemistry for labeling and detection of biomolecules. Molecular probes for biomedical applications II; 21 - 22 January 2008, San Jose, CA, USA; 6867, 1 - 686708 - 10.
21. Baskin, J. M., Prescher, J. A., Laughlin, S. T., Agard, N. J., Chang, P. V., Miller, I. A., Lo, A., Codelli, J. A., and Bertozzi, C. R. (2007) Copper-free click chemistry for dynamic in vivo imaging Proc. Natl. Acad. Sci. U.S.A. 104, 16793-16797
22. Froehler, B. C., Wadwani, S., Terhorst, T. J., and Gerrard, S. R. (1992) Oligodeoxynucleotides containing C-5 propyne analogs of 2′-deoxyuridine and 2′-deoxycytidine Tetrahedron Lett. 33, 5307-5310
23. Graham, D., Parkinson, J. A., and Brown, T. (1998) DNA duplexes stabilized by modified monomer residues: Synthesis and stability J. Chem. Soc., Perkin Trans. 1, 1131-1138
24. Sági, J., Szemzö, A., Ébinger, K., Szabolcs, A., Sági, G., Ruff, É., and Ötvös, L. (1993) Base-modified oligodeoxynucleotides. I: Effect of 5-alkyl, 5-(1-alkenyl) and 5-(1-alkynyl) substitution of the pyrimidines on duplex stability and hydrophobicity Tetrahedron Lett. 34, 2191-2194
25. Kottysch, T., Ahlborn, C., Brotzel, F., and Richert, C. (2004) Stabilizing or destabilizing oligodeoxynucleotide duplexes containing single 2′-deoxyuridine residues with 5-alkynyl substituents Chem. - Eur. J. 10, 4017-4028
26. Seela, F., Zulauf, M., and Debelak, H. (2000) Base-pairing properties of 8-aza-7-deazaadenine linked via the 8-position to the DNA backbone Helv. Chim. Acta 83, 1437-1453
27. Seela, F. and Debelak, H. (2001) 8-Aza-7-deazaadenine and 7-deazaguanine: Synthesis and properties of nucleosides and oligonucleotides with nucleobases linked at position-8 Nucleosides, Nucleotides Nucleic Acids 20, 577-585
28. Seela, F., Zulauf, M., Sauer, M., and Deimel, M. (2000) 7-Substituted 7-deaza-2′-deoxyadenosines and 8-aza-7-deaza-2′-deoxyadenosines: Fluorescence of DNA base analogues induced by the 7-alkynyl side chain Helv. Chim. Acta 83, 910-927
29. Seela, F. and Zulauf, M. (1998) Synthesis of 7-alkynylated 8-aza-7-deaza-2′-deoxy adenosines via the Pd-catalysed cross-coupling reaction J. Chem. Soc., Perkin Trans. 1, 3233-3239
30. He, J. and Seela, F. (2002) 8-Aza-7-deazapurine-pyrimidine base pairs: The contribution of 2- and 7-substituents to the stability of duplex DNA Tetrahedron 58, 4535-4542
31. He, J. and Seela, F. (2002) Propynyl groups in duplex DNA: Stability of base pairs incorporating 7-substituted 8-aza-7-deazapurines or 5-substituted pyrimidines Nucleic Acids Res. 30, 5485-5496
32. Seela, F., Jawalekar, A. M., Sun, L., and Leonard, P. (2005) Oligonucleotides containing pyrazolo[3,4-d]pyrimidines: 8-Aza-7-deazaadenines with bulky substituents in the 2- or 7-position Nucleosides, Nucleotides Nucleic Acids 24, 1485-1505
33. Wagenknecht, H.-A. (2006) Charge Transfer in DNA. Published by Wiley-VCH Verlag GmbH & Co. DOI: 10.1002/3527606629.
34. Latimer, L. J. P. and Lee, J. S. (1991) Ethidium Bromide does not fluoresce when intercalated adjacent to 7-deazaguanine in duplex DNA J. Biol. Chem. 266, 13849-13851
35. Li, H., Peng, X., and Seela, F. (2004) Fluorescence quenching of parallel-stranded DNA bound ethidium bromide: The effect of 7-deaza-2′- deoxyisoguanosine and 7-halogenated derivatives Bioorg. Med. Chem. Lett. 14, 6031-6034
36. Genereux, J. C. and Barton, J. K. (2010) Mechanisms for DNA charge transport. Chem. Rev. DOI:10.1021/cr900228f.
37. Seela, F. and Ingale, S. A. (2010) "Double Click" reaction on 7-deazaguanine DNA: Synthesis and excimer fluorescence of nucleosides and oligonucleotides with branched side chains decorated with proximal pyrenes J. Org. Chem. 75, 284-295
38. Seidel, C. A. M., Schulz, A., and Sauer, M. H. M. (1996) Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies J. Phys. Chem. 100, 5541-5553
39. 3 adenosine receptor agonists, partial agonists, and antagonists J. Med. Chem. 49, 7373-7383
40. Gierlich, J., Burley, G. A., Gramlich, P. M. E., Hammond, D. M., and Carell, T. (2006) Click chemistry as a reliable method for the high-density postsynthetic functionalization of alkyne-modified DNA Org. Lett. 17, 3639-3642
41. Seo, T. S., Li, Z., Ruparel, H., and Ju, J. (2003) Click chemistry to construct fluorescent oligonucleotides for DNA sequencing J. Org. Chem. 68, 609-612
42. Hainke, S. and Seitz, O. (2009) Binaphthyl-DNA: Stacking and fluorescence of a nonplanar aromatic base surrogate in DNA Angew. Chem., Int. Ed. 48, 8250-8253
43. Dose, C. and Seitz, O. (2008) Single nucleotide specific detection of DNA by native chemical ligation of fluorescence labeled PNA-probes Bioorg. Med. Chem. 16, 65-77
44. Chang, K.-C., Su, I.-H., Senthilvelan, A., and Chung, W.-S. (2007) Triazole-modified calix[4]crown as a novel fluorescent on-off switchable chemosensor Org. Lett. 9, 3363-3366
45. Stack, D. E., Hill, A. L., Diffendaffer, C. B., and Burns, N. M. (2002) Synthesis of a new fluorescent probe specific for catechols Org. Lett. 4, 4487-4490
46. Xie, F., Sivakumar, K., Zeng, Q., Bruckman, M. A., Hodges, B., and Wang, Q. (2008) A fluorogenic 'click' reaction of azidoanthracene derivatives Tetrahedron 64, 2906-2914
47. Sivakumar, K., Xie, F., Cash, B. M., Long, S., Barnhill, H. N., and Wang, Q. (2004) A fluorogenic 1,3-dipolar cycloaddition reaction of 3-azidocoumarins and acetylenes Org. Lett. 6, 4603-4606
48. Franzini, R. M. and Kool, E. T. (2008) 7-Azidomethoxy-coumarins as profluorophores for templated nucleic acid detection ChemBioChem 9, 2981-2988
49. Seela, F. and Sirivolu, V. R. (2007) Nucleosides and oligonucleotides with diynyl side chains: The Huisgen-Sharpless cycloaddition "click"reaction" performed on DNA and their constitutents Nucleosides, Nucleotides Nucleic Acids 26, 597-601
50. Seela, F. and Zulauf, M. (1999) Oligonucleotides containing 7-deazaadenines: The influence of the 7-substituent chain length and charge on the duplex stability Helv. Chim. Acta 82, 1878-1898
51. Becher, G., He, J., and Seela, F. (2001) Major-groove-halogenated DNA: The effects of bromo and iodo substituents replacing H-C(7) of 8-aza-7-deazapurine-2,6-diamine or H-C(5) of uracil residues Helv. Chim. Acta 84, 1048-1065
52. Seela, F. and Becher, G. (1999) Oligonucleotides containing pyrazolo[3,4-d]pyrimidines: The influence of 7-substituted 8-aza-7-deaza- 2′-deoxyguanosines on the duplex structure and stability Helv. Chim. Acta 82, 1640-1655
53. Seela, F. and Becher, G. (2001) Pyrazolo[3,4-d]pyrimidine nucleic acids: Adjustment of dA-dT to dG-dC base pair stability Nucleic Acids Res. 29, 2069-2078
54. Seela, F. and Shaikh, K. I. (2005) Oligonucleotides containing 7-propynyl-7-deazaguanine: Synthesis and base pair stability Tetrahedron 61, 2675-2681
55. Wagenknecht, H.-A. (2006) DNA as functional π-system: Electron transfer in synthetically modified oligonucleotides. Functional Organic Materials-Synthesis, strategies, and applications (Bunz, U. F. and Müller, T. T. J., Eds) pp 441 - 464, Wiley-VCH, Weinheim, Germany.
56. Wagenknecht, H.-A. (2006) Electron transfer processes in DNA: Mechanisms, biological relevance and applications in DNA analytics Nat. Prod. Rep. 23, 973-1006
57. Wagenknecht, H.-A. (2003) Reductive electron transfer and excess electron migration in DNA Angew. Chem., Int. Ed. 42, 2454-2460
58. Wilson, W. D., Wang, Y.-H., Kusuma, S., Chandrasekaran, S., Yang, N. C., and Boykin, D. W. (1985) Binding strength and specificity in DNA interactions: The design of A·T specific intercalators J. Am. Chem. Soc. 107, 4989-4995
59. Kumar, C. V. and Asuncion, E. H. (1993) DNA binding studies and site selective fluorescence sensitization of an anthryl probe J. Am. Chem. Soc. 115, 8547-8553
60. Duff, M. R., Jr., Mudhivarthi, V. K., and Kumar, C. V. (2009) Rational design of anthracene-based DNA binders J. Phys. Chem. B 113, 1710-1721