Drug-DNA Interaction Protocols by Keith R. Fox

By Keith R. Fox

A suite of invaluable molecular strategies to light up and discover the interplay of gear and ligands with DNA. those simply reproducible tools contain series acceptance 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 point of view and for his or her usefulness within the layout of latest healing brokers. The strong ideas designated right here may be rather invaluable in elucidating the motion of current healing brokers, in addition to within the layout of latest anti-cancer medicinal drugs with more suitable motion and decreased toxicity.

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25 0 05 042 From G-label gel The highest bmdmg constant found on the fragment, 6 x 106W1, occurs for the sequence S-TGCT-3’ at sites 136-139. The same sequence occurs at sites 62-65; the binding constant here 1sdetermined to be 4 x 1O6AR’. If, as 1sbelieved, bmdmg constants can be determmed to better accuracy than 50%, the difference between these two values ts real, implying that basesflankmg the tetramer may change its binding constant. As another example, the binding constant for the 5’-GCGC-3’ sequence at sites 101-l 04 was determmed as 2 x 1O6 M-* in this work, and quantitatrve footprinting studies of ActD bmdmg to the fragment d(TAGCGCTA), returned a value double this The discrepancy may be because of flanking sequences again, or to end effects associated (12) with short pieces of DNA.

7 x 1O5M-i, respectively. Although the average deviation between experimental and calculated intensities approached the estimated experimental error, the deviations in certain footprintmg plots remained significant. Some experimental plots had shapes that could not be explamed by the model. For example, mtensities for site 59, Fig. 3, modeled as an enhancement site, are roughly constant for drug concen- Quan tita We DNA Foo tprin ting 37 trations ~20 pA4,and also constant, but at about double the original value, for concentrations ~30 piH.

References 1 Burrows, H. D. and Kemp, T. J (1974) The photochemtstry of the uranyl ton. , Sonmchsen, S. , and Nordtn, B (1992) DNA Bmdmg and Photocleavage by Uranyl(V1) (UO,*‘) Salts J Amer Chem. Sot 114,4967-4975 Uranyl Photoprobrng 49 3 Nielsen, P. , and Buchardt, 0. (1988) Uranyl salts as photochemical agents for cleavage of DNA and probing of protein-DNA contacts. FEBSLett 235, 122-124 4 Jeppesen, C. and Nielsen, P (1989) Uranyl mediated photofootprmtmg reveals strong E cob RNA polymerase-DNA backbone contacts in the +lO region of the deoP1 promoter open complex.

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