PMID: 2105745Jan 16, 1990Paper

Drug binding by branched DNA molecules: analysis by chemical footprinting of intercalation into an immobile junction

Biochemistry
Q GuoN R Kallenbach

Abstract

Branched DNA structures interact with drugs differently from unbranched control duplexes of similar sequence. A specific interaction between the reagent (methidiumpropyl-EDTA).Fe(II) [MPE.Fe(II)] and a branched DNA molecule formed from 16-mer oligonucleotide strands has been reported [Guo, Q., Seeman, N. C., & Kallenbach, N. R. (1989) Biochemistry 28, 2355-2359]. The structure of the branched molecule is thought to be made up of two double-helical stacking domains with an overall twofold symmetry across the branch site. The MPE-Fe(II) interaction occurs predominantly at or adjacent to the branch site and is eliminated by a second intercalator, propidium iodide. Further studies on the nature and properties of this site are presented here. Comparison of the patterns of scission of linear duplex and branched tetramer by EDTA.Fe(II), MPE.Fe(II), and Cu(I)-(o-phenanthroline)2 [(OP)2Cu(I)] provides a higher resolution picture of the site of enhanced binding. In particular, the sensitive footprinting afforded by (OP)2Cu(I) allows us to localize the major site of preferential interaction with propidium precisely to the branch point itself, with a roughly twofold symmetric pattern of cuts resulting. In detail, the differential pattern w...Continue Reading

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Citations

Jun 1, 1994·Journal of Molecular Recognition : JMR·D M Lilley
Jun 14, 2002·Journal of Inorganic Biochemistry·Bidyut K SantraAkhil R Chakravarty
Oct 1, 1991·Journal of Biomolecular Structure & Dynamics·M LuN R Kallenbach
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Dec 11, 1990·Biochemistry·Q GuoN R Kallenbach
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Jan 1, 1992·Critical Reviews in Biochemistry and Molecular Biology·M LuN R Kallenbach
Jul 25, 1998·The Journal of Biological Chemistry·M C Whitby, R G Lloyd

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