By Keith R. Fox

A set of valuable molecular strategies to light up and discover the interplay of gear and ligands with DNA. those simply reproducible equipment contain series attractiveness houses, in addition to the actual techniques for measuring either the power of interplay and the mode of drug binding to DNA. The interactions also are tested from a mobile viewpoint and for his or her usefulness within the layout of latest healing brokers. The robust strategies specific the following should be quite beneficial in elucidating the motion of latest healing brokers, in addition to within the layout of recent anti-cancer medicinal drugs with more advantageous motion and lowered toxicity.

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This gives an Os04/pyridme mixture (4: 1, by vol) containing 25 mM 0~0,. The OsO,, solution turns yellow upon adding the pyridine. 1. DEPC Reaction The labeled DNA samples (100-500 cps) are diluted with the solution of the test drug prepared m 10 mA4Trts-HCl buffer (or other compatible buffer). The Drug-induced Changes in DNA Conformation 59 samples (20 pL) are left to equtlibrate for a mimmum of 30 mm at 37°C One microliter of DEPC is then added and the mrxture left at room temperature for a further 15 min with frequent mixing (DEPC 1snot mtscrble wtth water).

0~0~ can be purchased in a sealed ampoule contammg 250 mg (from Sigma or Aldrich for example). Because it 58 Bail/y and Waring is volatile, the ampoule containing the pale yellow solid has to be cooled down before opening. Addrtion of 2 mL of deionized water immediately after openmg the ampoule gives a 500-W stock solution, which is then diluted 1O-fold and dispensed mto 50-uL aliquots for storage at -2OOC. Frozen solutions of 0~0~ are relatively stable (for at least 6 mo). 2. DNA An important facet of a successful chemical probing experiment is the quality of the DNA.

Thus, as previously noted (3,4), the mformatlon obtained from uranyl photoprobmg m spite of the similarity of the footprints complements that of Fe/EDTA footprint, since the former reflects the accessiblhty of the backbone phosphates as well as the electrostatic potential, whereas the latter reflects the accessibility of the deoxyriboses of the backbone. 3’4abeled A/G1234 S-labeled 56 78 60 50 40 30 Fig. 1. Uranyl photofootprint of distamycin binding and probing of minor groove width in the &rT promoter.

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Drug-DNA Interaction Protocols by Keith R. Fox


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