Synthesis and properties of a novel fluorescent nucleobase, naphthopyridopyrimidine

Tetrahedron Letters

Volumn 44, Issue 36, 2003, Pages 6871-6874

  Okamoto, Akimitsu ^a   Tainaka, Kazuki ^a   Saito, Isao ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NAPHTHOPYRIDOPYRIDINE; NUCLEIC ACID BASE; PYRIDINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; FLUORESCENCE; GENE TARGETING; HYBRIDIZATION; PHYSICAL CHEMISTRY; QUANTUM YIELD; SYNTHESIS;

EID: 0042660814     PISSN: 00404039     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0040-4039(03)01740-4     Document Type: Article

References (16)

1. 2-Aminopurine: (a) Ward, D. C.; Reich, E.; Stryer, L. J. Biol. Chem. 1969, 244, 1228-1237; (b) Menger, M.; Tuschl, T.; Eckstein, F.; Porschke, D. Biochemistry 1996, 35, 14710-14716; (c) Lacourciere, K. A.; Stivers, J. T.; Marino, J. P. Biochemistry 2000, 39, 5630-5641.
2. 2-Aminopurine: (a) Ward, D. C.; Reich, E.; Stryer, L. J. Biol. Chem. 1969, 244, 1228-1237; (b) Menger, M.; Tuschl, T.; Eckstein, F.; Porschke, D. Biochemistry 1996, 35, 14710-14716; (c) Lacourciere, K. A.; Stivers, J. T.; Marino, J. P. Biochemistry 2000, 39, 5630-5641.
3. 2-Aminopurine: (a) Ward, D. C.; Reich, E.; Stryer, L. J. Biol. Chem. 1969, 244, 1228-1237; (b) Menger, M.; Tuschl, T.; Eckstein, F.; Porschke, D. Biochemistry 1996, 35, 14710-14716; (c) Lacourciere, K. A.; Stivers, J. T.; Marino, J. P. Biochemistry 2000, 39, 5630-5641.
4. 1,N-Ethenoadenosine: (a) Secrist, J. A., III; Barrio, J. R.; Leonard, N. J. Science 1972, 175, 646-647; (b) Holmén, A.; Albinsson, B.; Nordén, B. J. Phys. Chem. 1994, 98, 13460-13469 and references cited therein.
5. 1,N-Ethenoadenosine: (a) Secrist, J. A., III; Barrio, J. R.; Leonard, N. J. Science 1972, 175, 646-647; (b) Holmén, A.; Albinsson, B.; Nordén, B. J. Phys. Chem. 1994, 98, 13460-13469 and references cited therein.
6. Ethynyl-extended pyrimidines and deazapurines: (a) Seela, F.; Zulauf, M. ; Sauer, M.; Deimel, M. Helv. Chim. Acta 2000, 83, 910-927; (b) Hurley, D. J.; Seaman, S. E.; Mazura, J. C.; Tor, Y. Org. Lett. 2002, 4, 2305-2308.
7. Ethynyl-extended pyrimidines and deazapurines: (a) Seela, F.; Zulauf, M. ; Sauer, M.; Deimel, M. Helv. Chim. Acta 2000, 83, 910-927; (b) Hurley, D. J.; Seaman, S. E.; Mazura, J. C.; Tor, Y. Org. Lett. 2002, 4, 2305-2308.
8. Nucleoside analogs replaced by flat aromatic fluorophores: (a) Strässler, C.; Davis, N. E.; Kool, E. T. Helv. Chim. Acta 1999, 82, 2160-2171; (b) Kool, E. T. Acc. Chem. Res. 2002, 35, 936-943.
9. Nucleoside analogs replaced by flat aromatic fluorophores: (a) Strässler, C.; Davis, N. E.; Kool, E. T. Helv. Chim. Acta 1999, 82, 2160-2171; (b) Kool, E. T. Acc. Chem. Res. 2002, 35, 936-943.
10. Okamoto A., Tainaka K., Saito I. J. Am. Chem. Soc. 125:2003;4972-4973.
11. +] 380.1247, found 380.1247.
12. +] 682.2553, found 682.2558. To a solution of dimethoxytrityl-NPP (31 mg, 0.046 mmol) in acetonitrile (2 mL) was added 2-cyanoethyl tetraisopropyldiphosphoramidite (18 μL, 0.055 mmol) and tetrazole (4 mg, 0.055 mmol), and the mixture was stirred for 2 h at ambient temperature. The reaction mixture was filtrated and used with no further purification to the ODN synthesis step.
13. -] calcd 4004.65, found 4005.03.
14. m of the duplexes (2.5 μM) were measured in 50 mM sodium phosphate and 100 mM sodium chloride, pH 7.0. The absorbance of the duplexes was monitored at 260 nm from 2 to 80°C using a heating rate of 1°C/min.
15. ms of the natural base pairs A/T and G/C were 52.6 and 57.4°C, respectively.
16. The general utility of our method is limited by the flanking base pair of NPP. When the flanking base pair is a G/C base pair, the fluorescence of NPP is considerably suppressed. Thus, the SNP typing method would be inaccurate for the sequence containing a G/C base pair flanking the SNP site.