title: Atomic force microscopy study of the structural effects induced by echinomycin binding to DNA.
abstract: Atomic force microscopy (AFM) has been used to examine the conformational effects of echinomycin, a DNA bis-intercalating antibiotic, on linear and circular DNA. Four different 398 bp DNA fragments were synthesized, comprising a combination of normal and/or modified bases including 2,6-diaminopurine and inosine (which are the corresponding analogues of adenine and guanosine in which the 2-amino group that is crucial for echinomycin binding has been added or removed, respectively). Analysis of AFM images provided contour lengths, which were used as a direct measure of bis-intercalation. About 66 echinomycin molecules are able to bind to each fragment, corresponding to a site size of six base-pairs. The presence of base-modified nucleotides affects DNA conformation, as determined by the helical rise per base-pair. At the same time, the values obtained for the dissociation constant correlate with the types of preferred binding site available among the different DNA fragments; echinomycin binds to TpD sites much more tightly than to CpG sites. The structural perturbations induced when echinomycin binds to closed circular duplex pBR322 DNA were also investigated and a method for quantification of the structural changes is presented. In the presence of increasing echinomycin concentration, the plasmid can be seen to proceed through a series of transitions in which its supercoiling decreases, relaxes, and then increases.
authors.affiliation: Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
authors.forename: Yolanda D
authors.initials: YD
authors.lastname: Tseng
authors.forename: Haifang
authors.initials: H
authors.lastname: Ge
authors.forename: Xiuzhu
authors.initials: X
authors.lastname: Wang
authors.forename: J Michael
authors.initials: JM
authors.lastname: Edwardson
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Waring
authors.forename: William J
authors.initials: WJ
authors.lastname: Fitzgerald
authors.forename: Robert M
authors.initials: RM
authors.lastname: Henderson
mesh_terms: D015075:2-Aminopurine / Q000031:analogs & derivatives* / Q000494:pharmacology; D004247:DNA / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure*; D004270:DNA, Circular / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D004448:Echinomycin / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology*; D006860:Hydrogen Bonding / Q000187:drug effects; D007364:Intercalating Agents / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D008024:Ligands; D018625:Microscopy, Atomic Force; D009690:Nucleic Acid Conformation / Q000187:drug effects; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure
chemical_list: D004270:DNA, Circular; D007364:Intercalating Agents; D008024:Ligands; D015075:2-Aminopurine; C007300:2,6-diaminopurine; D004448:Echinomycin; D004247:DNA