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16
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3142748255
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note
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6]) for the duplex experiment (t-loop). The assay employs 96-well plates and used a DNA Engine Opticon instrument (MJ Research).
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17
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33845573936
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note
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Competition FRET experiments were performed as described above for the G-quadruplex experiment but with addition of varying concentrations of double strand DNA from calf thymus, c.t. dsDNA (Sigma-Aldrich, UK) (Moorhouse, A. D.; Santos, A. M.; Gunaratnam, M.; Moore, M.; Neidle, S.; Moses, J. E. J. Am. Chem. Soc. 2006, 128, 15972). The ct dsDNA has a length of about 200 bp and was obtained by sonication.
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19
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67649656788
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note
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32P-radiolabelled TS (0.16 μM final concentration) and 1 μl/sample of Primer Mix, 2U Taq DNA polymerase (Taq DNA polymerase/HotMaster™) were added in each sample. 30 PCR cycles were performed (94°/10′, 92°/30″, 54°/30″, 72°/5′30″). Finally, the samples were loaded on a native 12% polyacrylamide gel. Samples without the compound and without the cell-extract were used as references. A 36 bp oligonucleotide (IS) was used as internal standard to evaluate PCR amplification efficiency.
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20
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67649656789
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note
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13 The concentrations of DNAs started at 400 μM so to have a DNA/drug molar ratio R equal to 20 and then were decreased up to 0.5 μM, by substituting a volume of drug/DNA solutions with an equal volume of 20 μM drug solution. Absorption spectra were performed with a Varian Cary 50 spectrophotometer, using a cell with a 1 cm path length. Each spectrum was acquired after the sample has been equilibrated for at least 4 min.
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23
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67649648639
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note
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16 CD spectra were recorded on JASCO 710 dichrograph using a 1.0 cm path length cell. Each spectrum was acquired after the sample had been equilibrated for at least 4 min. For each sample, the scan of the buffer alone was subtracted from the average scan. The reported spectrum was averaged from at least four different scans.
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25
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39749136532
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Gottarelli G., Lena S., Masiero S., Pieraccini S., and Spada G.P. Chirality 20 (2008) 471
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Gottarelli, G.1
Lena, S.2
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Spada, G.P.5
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28
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34249846802
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Dai J., Punchihewa C., Ambrus A., Chen D., Jones R.A., and Yang D. Nucleic Acids Res. 35 (2007) 2440
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Dai, J.1
Punchihewa, C.2
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Yang, D.6
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