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Volumn , Issue 13, 2008, Pages 2220-2231

A neutral DNA sequence-selective vector for interaction studies: Fluorescence binding experiments directed towards a carbohydrate-DNA carrier

Author keywords

Carbohydrates; DNA recognition; Fluorescence spectroscopy; Vectors

Indexed keywords


EID: 53749087932     PISSN: 1434193X     EISSN: 10990690     Source Type: Journal    
DOI: 10.1002/ejoc.200701123     Document Type: Article
Times cited : (3)

References (93)
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    • The aromatic amino acid (Py) is known to be AT/TA-selective: S. White, E. E. Baird, P. B. Dervan, Biochemistry 1996, 35, 12532-12537.
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    • Determined by Wemmer in the bound state for larger oligoamide dimers such as Im-Py-Py-γ-Py-Py-Py-Dp; a C. A. Hawkins, R. P. de Clairac, R. N. Dominey, E. E. Baird, S. White, P. B. Dervan, D. E. Wemmer, J. Am. Chem. Soc. 2000, 122, 5235-5243
    • Determined by Wemmer in the bound state for larger oligoamide dimers such as Im-Py-Py-γ-Py-Py-Py-Dp; a) C. A. Hawkins, R. P. de Clairac, R. N. Dominey, E. E. Baird, S. White, P. B. Dervan, D. E. Wemmer, J. Am. Chem. Soc. 2000, 122, 5235-5243.
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    • All the compounds used in this paper were synthesized by the procedure described in ref.[49
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    • In order to exclude the possibility of self association in the concentration range of the fluorescence studies (0.1-3 mM, a dilution experiment by UV and fluorescence spectroscopy in the buffer/7, v/v) DMSO mixture was carried out with 4, 9, 10 and a 9/10 mixture (30:1) as models. The results showed that at ligand concentrations below 5×10 -6 M all the ligands are monomers
    • -6 M all the ligands are monomers.
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    • The interstrand nOes suggested that sugar-oligoamides each present a certain percentage of hairpin conformation in the free state, and TR-NOESY also suggested hairpin structures in the bound state
    • The interstrand nOes suggested that sugar-oligoamides each present a certain percentage of hairpin conformation in the free state, and TR-NOESY also suggested hairpin structures in the bound state.
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    • Under these conditions the sugar-oligoamide fluorescence quantum yield is at least ≈100% of its value in phosphate buffer solution. The refractive index of the aqueous buffer solution containing 7% (v/v) DMSO was therefore measured and the refractive index ratio was taken into account to determine the quantum yield for compound 4 and the models 1-3, 9-10.
    • Under these conditions the sugar-oligoamide fluorescence quantum yield is at least ≈100% of its value in phosphate buffer solution. The refractive index of the aqueous buffer solution containing 7% (v/v) DMSO was therefore measured and the refractive index ratio was taken into account to determine the quantum yield for compound 4 and the models 1-3, 9-10.
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    • Studies on the solvent effect for indole fluorescence quantum yields show that changing the solvent from the apolar cyclohexane or methylcyclohexane to a polar and H-bonding solvent such as methanol or propan-2-ol produces a reduction of one order of magnitude in the fluorescence quantum yield value of the indole; a S. C. Oh, Y. Shirota, J. Photochem. Photobiol. A 1995, 92, 79-83;
    • Studies on the solvent effect for indole fluorescence quantum yields show that changing the solvent from the apolar cyclohexane or methylcyclohexane to a polar and H-bonding solvent such as methanol or propan-2-ol produces a reduction of one order of magnitude in the fluorescence quantum yield value of the indole; a) S. C. Oh, Y. Shirota, J. Photochem. Photobiol. A 1995, 92, 79-83;
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    • -5 M concentration range. No chemical shift differences were detected, suggesting no aggregation behaviour.
    • -5 M concentration range. No chemical shift differences were detected, suggesting no aggregation behaviour.
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    • [49]
    • [49]
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    • This enhancement of the fluorescence intensity has previously been used to quantify the interaction of other DNA binders. J. B. Chaires, Methods in enzymology, Academic Press, San Diego, USA, 2001
    • This enhancement of the fluorescence intensity has previously been used to quantify the interaction of other DNA binders. J. B. Chaires, Methods in enzymology, Academic Press, San Diego, USA, 2001.
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    • -3 M for ml-DNA].
    • -3 M for ml-DNA].
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    • a values of the sugar-oligoamides are due to differences in the nature of the saccharide residue and not to cooperative binding, Hill plots for all the sugar oligoamide-poly(dA-dT) complexes were determined, and no cooperativity was found in any case (nH = 1); a) M. J. Jezewska, W. Bujalowski, Biophys. Chem. 1997, 64, 253-269;
    • a values of the sugar-oligoamides are due to differences in the nature of the saccharide residue and not to cooperative binding, Hill plots for all the sugar oligoamide-poly(dA-dT) complexes were determined, and no cooperativity was found in any case (nH = 1); a) M. J. Jezewska, W. Bujalowski, Biophys. Chem. 1997, 64, 253-269;
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    • see Figure S23 Supporting Information
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    • Comparisons are made with Ka values measured under conditions similar to ours: T = 20-27°C, pH = 7.0-7.4, [NaCl] < 0.1 M.
    • Comparisons are made with Ka values measured under conditions similar to ours: T = 20-27°C, pH = 7.0-7.4, [NaCl] < 0.1 M.
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    • This has been extensively studied; refs.[14,77-79
    • This has been extensively studied; refs.[14,77-79]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.