title: Dissociation of the AT-specific bifunctional intercalator [N-MeCys3,N-MeCys7]TANDEM from TpA sites in DNA.
abstract: We have examined the dissociation of [N-MeCys3,N-MeCys7]TANDEM, an AT-selective bifunctional intercalator, from TpA sites in mixed-sequence DNAs by a modification of the footprinting technique. Dissociation of complexes between the ligand and radiolabelled DNA fragments was initiated by adding a vast excess of unlabelled calf thymus DNA. Portions of this mixture were subjected to DNAse I footprinting at various times after adding the competitor DNA. Dissociation of the ligand from each site was seen by the time-dependent disappearance of the footprinting pattern. Within a natural DNA fragment (tyrT) the ligand dissociates from TTAT faster than from ATAT. We found that the stability of complexes with isolated TpA steps decreases in the order ATAT > TTAA > TATA. Dissociation from each of these sites is much faster than from longer regions of (AT)n. These results confirm the requirement for A and T base-pairs surrounding the TpA step and suggest that the interaction is strongest with regions of alternating AT, possibly as a result of its unusual structure. The ligand dissociates more slowly from the centre of (AT)n tracts than from the edges, suggesting that variations in dissociation rate arise from sequence-dependent variations in local DNA structure.
authors.affiliation: Department of Physiology and Pharmacology, Bassett Crescent East, University of Southampton, U.K.
authors.forename: M C
authors.initials: MC
authors.lastname: Fletcher
authors.forename: R K
authors.initials: RK
authors.lastname: Olsen
authors.forename: K R
authors.initials: KR
authors.lastname: Fox
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002417:Cattle; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D007364:Intercalating Agents / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D011810:Quinoxalines / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D007364:Intercalating Agents; D011810:Quinoxalines; C075619:(N-MeCys(3)-N-MeCys(7))TANDEM; D004247:DNA