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Volumn 126, Issue 31, 2004, Pages 9601-9610

2,2,5,5-Tetramethylpyrrolidin-3-one-1-sulfinyl group for 5′-hydroxyl protection of deoxyribonucleoside phosphoramidites in the solid-phase preparation of DNA oligonucleotides

Author keywords

[No Author keywords available]

Indexed keywords

ARRAYS; BACTERIA; GLASS; HYDROLYSIS; IODINE; NITROGEN COMPOUNDS; NUCLEIC ACIDS; SALTS; SULFUR COMPOUNDS; SYNTHESIS (CHEMICAL);

EID: 3543140734     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja048377i     Document Type: Article
Times cited : (7)

References (62)
  • 7
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    • For recent reviews on the immobilization of DNA on arrayable surfaces, see: (a) Pirrung, M. C. Angew. Chem., Int. Ed. 2002, 41, 1276-1289.
    • (2002) Angew. Chem., Int. Ed. , vol.41 , pp. 1276-1289
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    • 0035803031 scopus 로고    scopus 로고
    • This strategy has been explored by others in an effort to eliminate the use of protic acids in solid-phase oligonucleotide synthesis, see: (a) Seio, K.; Sekine, M. Tetrahedron Lett. 2001, 42, 8657-8660.
    • (2001) Tetrahedron Lett. , vol.42 , pp. 8657-8660
    • Seio, K.1    Sekine, M.2
  • 31
    • 3543114676 scopus 로고    scopus 로고
    • note
    • It should however be understood that our findings are aimed at improving the current methods for the synthesis of oligonucleotides on microarrays. In this regard, replacement of the DMTr group with an aminosulfinyl group should not be viewed as a loss of a color-producing indicator for phosphoramidite coupling efficiency given that the DMTr assay is not sensitive enough to reliably assess phosphoramidite coupling efficiency on microarrays.
  • 32
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    • Ger. Patent 1,150,994, July 4, 1963
    • (a) Weiss, G.; Schulze, G. Ger. Patent 1,150,994, July 4, 1963; Chem. Abstr. 1964, 60, 2956d.
    • (1964) Chem. Abstr. , vol.60
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    • note
    • 3N (3 mol equiv) in MeCN under an inert atmosphere at 5 °C.
  • 36
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    • note
    • 3N (3.3 mol equiv) in MeCN under an atmosphere of argon gas.
  • 37
    • 3543087694 scopus 로고    scopus 로고
    • note
    • Alternatively, 2,2,5,5-tetramethyl-3-pyrroline-3-carboxamide is inexpensively prepared in two steps from 2,2,6,6-tetramethylpiperidin-4-one.25a
  • 41
    • 0000904633 scopus 로고    scopus 로고
    • Barton, D., Nakanishi, K., Meth-Cohn, O., Kool, E. T., Eds.; Elsevier Science: London, U.K. (DNA and Aspects of Molecular Biology)
    • (b) Iyer, R. P.; Beaucage, S. L. In Comprehensive Natural Products Chemistry; Barton, D., Nakanishi, K., Meth-Cohn, O., Kool, E. T., Eds.; Elsevier Science: London, U.K., 1999; Vol. 7 (DNA and Aspects of Molecular Biology), pp 105-152.
    • (1999) Comprehensive Natural Products Chemistry , vol.7 , pp. 105-152
    • Iyer, R.P.1    Beaucage, S.L.2
  • 42
    • 3543057250 scopus 로고    scopus 로고
    • Beaucage, S. L., Bergstrom, D. E., Glick, G. D., Jones, R. A., Eds.; John Wiley & Sons: New York
    • (c) Seliger, H. In Current Protocols in Nucleic Acid Chemistry; Beaucage, S. L., Bergstrom, D. E., Glick, G. D., Jones, R. A., Eds.; John Wiley & Sons: New York, 2000; pp 2.3.1-2.3.34.
    • (2000) Current Protocols in Nucleic Acid Chemistry
    • Seliger, H.1
  • 46
    • 3543119222 scopus 로고    scopus 로고
    • note
    • The most important parameters investigated were (i) phosphoramidite coupling time and coupling efficiency, and (ii) time required for oxidative 5′-O-deprotection relative to the concentration of the acidic salt being used in the reaction.
  • 48
    • 0032577715 scopus 로고    scopus 로고
    • a of 4,5-dicyanoimidazole is 5.2, whereas that of 1H-tetrazole is 4.8, see: Jin, Y.; Just, G. J. Org. Chem. 1998, 63, 3647-3654.
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    • note
    • The details of this complex deprotection mechanism are still being investigated.
  • 50
    • 3543132148 scopus 로고    scopus 로고
    • note
    • Skipping the 1 min treatment with a commercial iodine solution leads to premature cleavage of the internucleoside phosphite triester linkage caused by the acidity of the 0.1 M iodine solution.
  • 51
    • 3543058418 scopus 로고    scopus 로고
    • note
    • 2O (9:1 v/v) results in a noticeably slower deprotection of the 5′-O-sulfinyl group and thus underscores the synergistic participation of iodine in the cleavage of the protecting group.
  • 53
    • 0000839769 scopus 로고
    • Iyer, R. P.; Phillips, L. R.; Egan, W.; Regan, J. B.; Beaucage, S. L. J. Org. Chem. 1990, 55, 4693-4699. See also: Regan, J. B.; Phillips, L. R.; Beaucage, S. L. Org. Prep. Proc. Int. 1992, 24, 488-492.
    • (1992) Org. Prep. Proc. Int. , vol.24 , pp. 488-492
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  • 54
    • 3543093582 scopus 로고    scopus 로고
    • note
    • PST) is provided in the Supporting Information and compared with a chromatogram of the same oligonucleotide synthesized from standard 5′-O-DMTr-deoxyribonucleoside phosphoramidites under similar conditions.
  • 59
    • 3543122680 scopus 로고    scopus 로고
    • note
    • These additional extractions are required only to optimize the recovery of 7b.
  • 60
    • 3543148648 scopus 로고    scopus 로고
    • note
    • 3. These signals are consistent with the four diastereomers emerging from the asymmetry of the phosphorus and sulfur atoms.


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